CudaSPONGE高性能GPU分子模拟
技术背景
CudaSPONGE是基于CUDA C开发的一款纯GPU分子动力学模拟软件，具有模块化和高性能的特点。官方基本介绍内容如下：
分子动力学（Molecular Dynamics, MD）模拟是化学、物理学、生物学、材料科学和许多其他领域的有用工具。在过去 40 年中，人们开发了各种高效的计算算法和MD程序，用于研究日益复杂和大型系统的动力学，如RNA 聚合酶、细胞膜中的膜蛋白、SARS-CoV-2病毒等。然而，随着应用范围和规模的扩大，分子模拟软件需要更高的计算能力。缩小模拟与实验之间差距的最直接策略是利用更强大的计算硬件。例如，Shaw研究所专门设计了安东（Anton），可以对系统大小为几百万个原子的单结构域蛋白质进行毫秒级模拟。相比之下，使用图形处理单元（GPU）可能是大多数研究小组最经济实惠和最有前途的方法。从另一个方面看，许多先进的计算算法也已开发出来并得到广泛应用，从而延长了模拟时间尺度。特别是在过去几十年中，人们开发了许多增强型采样方法，以实现快速热力学和/或动力学计算。这些方法包括但不限于广泛使用的伞状采样、元动力学、加速MD、复制交换分子动力学（REMD）、并行回火、模拟回火、多正则模拟（特别是通过Wang-Landau算法实现）以及许多其他方法。
在过去的 15 年中，我们致力于开发面向复杂化学和生物系统的高效分子模拟方法，设计了一系列增强型采样方法，实现了构象和轨迹空间的快速采样，并实现了复杂系统热力学和动力学特性的快速计算。 最近，我们开发了一个名为 SPONGE的国产MD模拟软件包，它不仅实现了GPU加速的传统MD模拟，还实现了我们课题组提出的高效增强采样方法。 该软件包具有高度模块化的特点，可以轻松集成其他功能或算法，尤其是最新的深度学习潜力和算法。
安装介绍
首先进到
CudaSPONGE官网
，找到最新版本的软件包下载到本地目录，主要依赖于
nvcc
进行编译构建。解包之后可以看到这样的目录：
$ ll
total 220
drwxrwxrwx 1 root root 4096 Sep 11 08:19 ./
drwxrwxrwx 1 root root 4096 Sep 11 08:19 ../
drwxrwxrwx 1 root root 4096 Sep 11 08:19 Lennard_Jones_force/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 MD_core/
-rwxrwxrwx 1 root root 3072 Jan 1 2024 Makefile*
drwxrwxrwx 1 root root 4096 Sep 11 08:19 No_PBC/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 PME_force/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 SITS/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 angle/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 barostats/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 bias/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 bond/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 cmap/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 collective_variable/
-rwxrwxrwx 1 root root 8311 Jan 1 2024 common.cu*
-rwxrwxrwx 1 root root 58097 Jan 1 2024 common.cuh*
drwxrwxrwx 1 root root 4096 Sep 11 08:19 constrain/
-rwxrwxrwx 1 root root 41504 Jan 1 2024 control.cu*
-rwxrwxrwx 1 root root 9465 Jan 1 2024 control.cuh*
drwxrwxrwx 1 root root 4096 Sep 11 08:19 covid-tip4p/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 dihedral/
-rwxrwxrwx 1 root root 34743 Jan 1 2024 jit.cuh*
-rwxrwxrwx 1 root root 32719 Jan 1 2024 main.cu*
-rwxrwxrwx 1 root root 2011 Jan 1 2024 main.cuh*
-rwxrwxrwx 1 root root 3408 Jan 1 2024 main_ti.cu*
-rwxrwxrwx 1 root root 489 Jan 1 2024 main_ti.cuh*
-rwxrwxrwx 1 root root 492 Jan 1 2024 mdin.txt*
drwxrwxrwx 1 root root 4096 Sep 11 08:19 nb14/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 neighbor_list/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 plugin/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 restrain/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 thermostats/
drwxrwxrwx 1 root root 4096 Sep 11 08:19 virtual_atoms/
-rwxrwxrwx 1 root root 11843 Jan 1 2024 vs_project_generator.bat*
drwxrwxrwx 1 root root 4096 Sep 11 08:19 wall/
然后可以在这个路径下直接执行：
$ make
过程中大致输出为：
编译输出
$ make
/bin/sh: bc: command not found
/bin/sh: bc: command not found
analyzing dependency of PME_force/cross_PME.cu to PME_force/cross_PME.d
analyzing dependency of PME_force/PME_force.cu to PME_force/PME_force.d
analyzing dependency of Lennard_Jones_force/LJ_soft_core.cu to Lennard_Jones_force/LJ_soft_core.d
analyzing dependency of neighbor_list/neighbor_list.cu to neighbor_list/neighbor_list.d
analyzing dependency of MD_core/MD_core.cu to MD_core/MD_core.d
analyzing dependency of control.cu to control.d
analyzing dependency of common.cu to common.d
analyzing dependency of main_ti.cu to main_ti.d
analyzing dependency of plugin/plugin.cu to plugin/plugin.d
analyzing dependency of wall/soft_wall.cu to wall/soft_wall.d
analyzing dependency of wall/hard_wall.cu to wall/hard_wall.d
analyzing dependency of bias/Meta1D.cu to bias/Meta1D.d
analyzing dependency of bias/steer.cu to bias/steer.d
analyzing dependency of bias/restrain_cv.cu to bias/restrain_cv.d
analyzing dependency of collective_variable/combine.cu to collective_variable/combine.d
analyzing dependency of collective_variable/tabulated.cu to collective_variable/tabulated.d
analyzing dependency of collective_variable/RMSD.cu to collective_variable/RMSD.d
analyzing dependency of collective_variable/simple_cv.cu to collective_variable/simple_cv.d
analyzing dependency of collective_variable/collective_variable.cu to collective_variable/collective_variable.d
analyzing dependency of SITS/SITS.cu to SITS/SITS.d
analyzing dependency of virtual_atoms/virtual_atoms.cu to virtual_atoms/virtual_atoms.d
analyzing dependency of constrain/SHAKE.cu to constrain/SHAKE.d
analyzing dependency of constrain/SETTLE.cu to constrain/SETTLE.d
analyzing dependency of constrain/simple_constrain.cu to constrain/simple_constrain.d
analyzing dependency of constrain/constrain.cu to constrain/constrain.d
analyzing dependency of restrain/restrain.cu to restrain/restrain.d
analyzing dependency of barostats/andersen_barostat.cu to barostats/andersen_barostat.d
analyzing dependency of barostats/Berendsen_barostat.cu to barostats/Berendsen_barostat.d
analyzing dependency of barostats/MC_barostat.cu to barostats/MC_barostat.d
analyzing dependency of thermostats/nose_hoover_chain.cu to thermostats/nose_hoover_chain.d
analyzing dependency of thermostats/Berendsen_thermostat.cu to thermostats/Berendsen_thermostat.d
analyzing dependency of thermostats/Andersen_thermostat.cu to thermostats/Andersen_thermostat.d
analyzing dependency of thermostats/Middle_Langevin_MD.cu to thermostats/Middle_Langevin_MD.d
analyzing dependency of thermostats/Langevin_MD.cu to thermostats/Langevin_MD.d
analyzing dependency of Lennard_Jones_force/pairwise_force.cu to Lennard_Jones_force/pairwise_force.d
analyzing dependency of Lennard_Jones_force/solvent_LJ.cu to Lennard_Jones_force/solvent_LJ.d
analyzing dependency of Lennard_Jones_force/Lennard_Jones_force.cu to Lennard_Jones_force/Lennard_Jones_force.d
analyzing dependency of No_PBC/Lennard_Jones_force_No_PBC.cu to No_PBC/Lennard_Jones_force_No_PBC.d
analyzing dependency of No_PBC/generalized_Born.cu to No_PBC/generalized_Born.d
analyzing dependency of No_PBC/Coulomb_Force_No_PBC.cu to No_PBC/Coulomb_Force_No_PBC.d
analyzing dependency of nb14/nb14.cu to nb14/nb14.d
analyzing dependency of cmap/cmap.cu to cmap/cmap.d
analyzing dependency of dihedral/improper_dihedral.cu to dihedral/improper_dihedral.d
analyzing dependency of dihedral/dihedral.cu to dihedral/dihedral.d
analyzing dependency of angle/Urey_Bradley_force.cu to angle/Urey_Bradley_force.d
analyzing dependency of angle/angle.cu to angle/angle.d
analyzing dependency of bond/listed_forces.cu to bond/listed_forces.d
analyzing dependency of bond/bond_soft.cu to bond/bond_soft.d
analyzing dependency of bond/bond.cu to bond/bond.d
analyzing dependency of main.cu to main.d
/bin/sh: bc: command not found
/bin/sh: bc: command not found
nvcc -o main.o -c main.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o common.o -c common.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o control.o -c control.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o MD_core/MD_core.o -c MD_core/MD_core.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/config.h:27:0,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config.h:23,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:24,
from MD_core/MD_core.cu:2:
/usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/cpp_dialect.h:131:13: warning: Thrust requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define THRUST_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message.
THRUST_COMPILER_DEPRECATION_SOFT(C++14, C++11);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_arch.cuh:36:0,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/detail/device_synchronize.cuh:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/util.h:36,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/for_each.h:35,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/adl/for_each.h:42,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/for_each.inl:27,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/for_each.h:277,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.inl:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.h:104,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/transform.inl:27,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/transform.h:721,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.inl:31,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.h:87,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/reduce.inl:28,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/reduce.h:781,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.inl:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.h:61,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/find.inl:25,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/find.h:381,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.inl:26,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.h:152,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/sort.inl:26,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:1358,
from MD_core/MD_core.cu:2:
/usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_cpp_dialect.cuh:142:13: warning: CUB requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define CUB_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message.
CUB_COMPILER_DEPRECATION_SOFT(C++14, C++11);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/config.h:27:0,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config.h:23,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:24,
from MD_core/MD_core.cu:2:
/usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/cpp_dialect.h:131:13: warning: Thrust requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define THRUST_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message.
THRUST_COMPILER_DEPRECATION_SOFT(C++14, C++11);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_arch.cuh:36:0,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/detail/device_synchronize.cuh:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/util.h:36,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/for_each.h:35,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/adl/for_each.h:42,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/for_each.inl:27,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/for_each.h:277,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.inl:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.h:104,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/transform.inl:27,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/transform.h:721,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.inl:31,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.h:87,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/reduce.inl:28,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/reduce.h:781,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.inl:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.h:61,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/find.inl:25,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/find.h:381,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.inl:26,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.h:152,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/sort.inl:26,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:1358,
from MD_core/MD_core.cu:2:
/usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_cpp_dialect.cuh:142:13: warning: CUB requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define CUB_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message.
CUB_COMPILER_DEPRECATION_SOFT(C++14, C++11);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nvcc -o bond/bond.o -c bond/bond.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o bond/bond_soft.o -c bond/bond_soft.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o bond/listed_forces.o -c bond/listed_forces.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o angle/angle.o -c angle/angle.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o angle/Urey_Bradley_force.o -c angle/Urey_Bradley_force.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o dihedral/dihedral.o -c dihedral/dihedral.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o dihedral/improper_dihedral.o -c dihedral/improper_dihedral.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o cmap/cmap.o -c cmap/cmap.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o nb14/nb14.o -c nb14/nb14.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o neighbor_list/neighbor_list.o -c neighbor_list/neighbor_list.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/config.h:27:0,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config.h:23,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:24,
from neighbor_list/neighbor_list.cu:2:
/usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/cpp_dialect.h:131:13: warning: Thrust requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define THRUST_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message.
THRUST_COMPILER_DEPRECATION_SOFT(C++14, C++11);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_arch.cuh:36:0,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/detail/device_synchronize.cuh:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/util.h:36,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/for_each.h:35,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/adl/for_each.h:42,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/for_each.inl:27,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/for_each.h:277,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.inl:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.h:104,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/transform.inl:27,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/transform.h:721,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.inl:31,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.h:87,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/reduce.inl:28,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/reduce.h:781,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.inl:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.h:61,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/find.inl:25,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/find.h:381,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.inl:26,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.h:152,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/sort.inl:26,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:1358,
from neighbor_list/neighbor_list.cu:2:
/usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_cpp_dialect.cuh:142:13: warning: CUB requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define CUB_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message.
CUB_COMPILER_DEPRECATION_SOFT(C++14, C++11);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/config.h:27:0,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config.h:23,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:24,
from neighbor_list/neighbor_list.cu:2:
/usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/config/cpp_dialect.h:131:13: warning: Thrust requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define THRUST_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message.
THRUST_COMPILER_DEPRECATION_SOFT(C++14, C++11);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_arch.cuh:36:0,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/cub/detail/device_synchronize.cuh:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/util.h:36,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/cuda/detail/for_each.h:35,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/adl/for_each.h:42,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/for_each.inl:27,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/for_each.h:277,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.inl:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/transform.h:104,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/transform.inl:27,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/transform.h:721,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.inl:31,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/reduce_by_key.h:87,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/reduce.inl:28,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/reduce.h:781,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.inl:19,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/find.h:61,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/find.inl:25,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/find.h:381,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.inl:26,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/system/detail/generic/sort.h:152,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/detail/sort.inl:26,
from /usr/local/cuda/bin/../targets/x86_64-linux/include/thrust/sort.h:1358,
from neighbor_list/neighbor_list.cu:2:
/usr/local/cuda/bin/../targets/x86_64-linux/include/cub/util_cpp_dialect.cuh:142:13: warning: CUB requires at least C++14. C++11 is deprecated but still supported. C++11 support will be removed in a future release. Define CUB_IGNORE_DEPRECATED_CPP_DIALECT to suppress this message.
CUB_COMPILER_DEPRECATION_SOFT(C++14, C++11);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nvcc -o No_PBC/Coulomb_Force_No_PBC.o -c No_PBC/Coulomb_Force_No_PBC.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o No_PBC/generalized_Born.o -c No_PBC/generalized_Born.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o No_PBC/Lennard_Jones_force_No_PBC.o -c No_PBC/Lennard_Jones_force_No_PBC.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o Lennard_Jones_force/Lennard_Jones_force.o -c Lennard_Jones_force/Lennard_Jones_force.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o Lennard_Jones_force/solvent_LJ.o -c Lennard_Jones_force/solvent_LJ.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o Lennard_Jones_force/LJ_soft_core.o -c Lennard_Jones_force/LJ_soft_core.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o Lennard_Jones_force/pairwise_force.o -c Lennard_Jones_force/pairwise_force.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o PME_force/PME_force.o -c PME_force/PME_force.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o thermostats/Langevin_MD.o -c thermostats/Langevin_MD.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o thermostats/Middle_Langevin_MD.o -c thermostats/Middle_Langevin_MD.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o thermostats/Andersen_thermostat.o -c thermostats/Andersen_thermostat.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o thermostats/Berendsen_thermostat.o -c thermostats/Berendsen_thermostat.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o thermostats/nose_hoover_chain.o -c thermostats/nose_hoover_chain.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o barostats/MC_barostat.o -c barostats/MC_barostat.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o barostats/Berendsen_barostat.o -c barostats/Berendsen_barostat.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o barostats/andersen_barostat.o -c barostats/andersen_barostat.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o restrain/restrain.o -c restrain/restrain.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o constrain/constrain.o -c constrain/constrain.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o constrain/simple_constrain.o -c constrain/simple_constrain.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o constrain/SETTLE.o -c constrain/SETTLE.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o constrain/SHAKE.o -c constrain/SHAKE.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o virtual_atoms/virtual_atoms.o -c virtual_atoms/virtual_atoms.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o SITS/SITS.o -c SITS/SITS.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o collective_variable/collective_variable.o -c collective_variable/collective_variable.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o collective_variable/simple_cv.o -c collective_variable/simple_cv.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o collective_variable/RMSD.o -c collective_variable/RMSD.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o collective_variable/tabulated.o -c collective_variable/tabulated.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o collective_variable/combine.o -c collective_variable/combine.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o bias/restrain_cv.o -c bias/restrain_cv.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o bias/steer.o -c bias/steer.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o bias/Meta1D.o -c bias/Meta1D.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o wall/hard_wall.o -c wall/hard_wall.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o wall/soft_wall.o -c wall/soft_wall.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o plugin/plugin.o -c plugin/plugin.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
sed -i 's/\r//' mdin.txt
sed -i 's/\r//' covid-tip4p/*
nvcc -o SPONGE main.o common.o control.o MD_core/MD_core.o bond/bond.o bond/bond_soft.o bond/listed_forces.o angle/angle.o angle/Urey_Bradley_force.o dihedral/dihedral.o dihedral/improper_dihedral.o cmap/cmap.o nb14/nb14.o neighbor_list/neighbor_list.o No_PBC/Coulomb_Force_No_PBC.o No_PBC/generalized_Born.o No_PBC/Lennard_Jones_force_No_PBC.o Lennard_Jones_force/Lennard_Jones_force.o Lennard_Jones_force/solvent_LJ.o Lennard_Jones_force/LJ_soft_core.o Lennard_Jones_force/pairwise_force.o PME_force/PME_force.o thermostats/Langevin_MD.o thermostats/Middle_Langevin_MD.o thermostats/Andersen_thermostat.o thermostats/Berendsen_thermostat.o thermostats/nose_hoover_chain.o barostats/MC_barostat.o barostats/Berendsen_barostat.o barostats/andersen_barostat.o restrain/restrain.o constrain/constrain.o constrain/simple_constrain.o constrain/SETTLE.o constrain/SHAKE.o virtual_atoms/virtual_atoms.o SITS/SITS.o collective_variable/collective_variable.o collective_variable/simple_cv.o collective_variable/RMSD.o collective_variable/tabulated.o collective_variable/combine.o bias/restrain_cv.o bias/steer.o bias/Meta1D.o wall/hard_wall.o wall/soft_wall.o plugin/plugin.o -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o main_ti.o -c main_ti.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o PME_force/cross_PME.o -c PME_force/cross_PME.cu -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
nvcc -o SPONGE_TI main_ti.o common.o control.o MD_core/MD_core.o neighbor_list/neighbor_list.o Lennard_Jones_force/LJ_soft_core.o PME_force/PME_force.o PME_force/cross_PME.o -rdc=true -lcudadevrt -lcuda -lcudart -lcufft -lnvrtc --use_fast_math -O4 -ldl -std=c++11 -arch=sm_50 -DCUDA_ARCH_BIN=50
即可完成
CudaSPONGE
的编译构建，在当前路径下生成一个
SPONGE
可执行文件：
$ ll | grep SPONGE
-rwxr-xr-x 1 root root 32455648 Nov 27 01:44 SPONGE*
-rwxr-xr-x 1 root root 7482232 Nov 27 01:44 SPONGE_TI*
预处理
为了使得工作空间更加分明，这里我建议先创建一个独立的工作区：
$ mkdir work_dir
准备一个待模拟的体系，例如我们这里使用一个简单的pdb纯蛋白体系：
REMARK Generated By Xponge (Molecule)
ATOM 1 N ALA 1 -0.095 -11.436 -0.780
ATOM 2 CA ALA 1 -0.171 -10.015 -0.507
ATOM 3 CB ALA 1 1.201 -9.359 -0.628
ATOM 4 C ALA 1 -1.107 -9.319 -1.485
ATOM 5 O ALA 1 -1.682 -9.960 -2.362
ATOM 6 N ARG 2 -1.303 -8.037 -1.397
ATOM 7 CA ARG 2 -2.194 -7.375 -2.328
ATOM 8 CB ARG 2 -3.606 -7.943 -2.235
ATOM 9 CG ARG 2 -4.510 -7.221 -3.228
ATOM 10 CD ARG 2 -5.923 -7.789 -3.136
ATOM 11 NE ARG 2 -6.831 -7.111 -4.087
ATOM 12 CZ ARG 2 -8.119 -7.421 -4.205
ATOM 13 NH1 ARG 2 -8.686 -8.371 -3.468
ATOM 14 NH2 ARG 2 -8.844 -6.747 -5.093
ATOM 15 C ARG 2 -2.273 -5.882 -2.042
ATOM 16 O ARG 2 -1.630 -5.388 -1.119
ATOM 17 N ALA 3 -3.027 -5.119 -2.777
ATOM 18 CA ALA 3 -3.103 -3.697 -2.505
ATOM 19 CB ALA 3 -1.731 -3.041 -2.625
ATOM 20 C ALA 3 -4.039 -3.001 -3.483
ATOM 21 O ALA 3 -4.614 -3.643 -4.359
ATOM 22 N ALA 4 -4.235 -1.719 -3.394
ATOM 23 CA ALA 4 -5.126 -1.057 -4.325
ATOM 24 CB ALA 4 -6.538 -1.625 -4.233
ATOM 25 C ALA 4 -5.205 0.436 -4.039
ATOM 26 O ALA 4 -4.561 0.930 -3.116
ATOM 27 OXT ALA 4 -5.915 1.166 -4.728
TER
因为pdb格式经常会面临文件不完整的问题，所以需要使用Xponge进行预处理，安装方法如下：
$ python3 -m pip install xponge --upgrade
文件处理的流程，这里用
ipython
的交互结果做一个简单的演示：
In [1]: import Xponge
In [2]: import Xponge.forcefield.amber.ff14sb # 导入力场
Reference for ff14SB:
James A. Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E. Hauser, and Carlos Simmerling
ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB
Journal of Chemical Theory and Computation 2015 11 (8), 3696-3713
DOI: 10.1021/acs.jctc.5b00255
In [3]: C = Xponge.load_pdb("case1.pdb", ignore_hydrogen=False, ignore_unknown_name=True) # 加载pdb文件
In [4]: C.add_missing_atoms() # 补齐氢原子和其他丢失的residue atom
In [5]: Xponge.save_pdb(C, "case1_fix.pdb") # 将新的体系保存到pdb文件中
In [7]: !mkdir protein
In [8]: Xponge.save_sponge_input(C, "protein/case1") # 保存SPONGE模拟所需参数文件
Reference for Xponge:
Xia, Y., Gao, Y. Q.
Xponge: A Python package to perform pre- and post-processing of molecular simulations
Journal of Open Source Software, 2022 7(77) 4467
DOI: 10.21105/joss.04467
Out[8]: Entity of Molecule: case1
In [10]: !ls -l protein/
total 32
-rwxr-xr-x 1 root root 1361 Nov 27 01:34 case1_LJ.txt
-rwxr-xr-x 1 root root 2717 Nov 27 01:34 case1_angle.txt
-rwxr-xr-x 1 root root 185 Nov 27 01:34 case1_atom_name.txt
-rwxr-xr-x 1 root root 153 Nov 27 01:34 case1_atom_type_name.txt
-rwxr-xr-x 1 root root 1437 Nov 27 01:34 case1_bond.txt
-rwxr-xr-x 1 root root 544 Nov 27 01:34 case1_charge.txt
-rwxr-xr-x 1 root root 1639 Nov 27 01:34 case1_coordinate.txt
-rwxr-xr-x 1 root root 4298 Nov 27 01:34 case1_dihedral.txt
-rwxr-xr-x 1 root root 977 Nov 27 01:34 case1_exclude.txt
-rwxr-xr-x 1 root root 371 Nov 27 01:34 case1_mass.txt
-rwxr-xr-x 1 root root 3197 Nov 27 01:34 case1_nb14.txt
-rwxr-xr-x 1 root root 16 Nov 27 01:34 case1_residue.txt
-rwxr-xr-x 1 root root 20 Nov 27 01:34 case1_resname.txt
这里除了补齐丢失的原子之外，还涉及到
CudaSPONGE
输入文件的问题，因此用Xponge来处理会相对便捷一些。到这里，就完成了
CudaSPONGE
分子模拟的预处理。
能量极小化
对于不同的模拟方法，我们需要给SPONGE输入不同的配置文件，例如能量最小化的一个配置文件的简单形式为
minimize.txt
：
case1 Minimization
mode = Minimization
minimization_dynamic_dt 1
default_in_file_prefix = protein/case1
pbc=0
cutoff=999
dt = 1e-02
step_limit = 5000
write_information_interval = 50
rst = restart
coordinate_in_file = protein/case1_coordinate.txt
在这个配置文件下，我们执行能量极小化的
mode
，参数文件保存在
protein/
目录下，并以
case1
开头。而模拟系统的笛卡尔坐标，由文件
protein/case1_coordinate.txt
给出。这个设置方便的地方在于，因为我们设置了
restart
参数，所以模拟结束之后会在当前路径下保存一个
restart_coordinate.txt
重启文件，所以下一次启动模拟的时候，只要把启动文件指向到这个restart坐标文件就可以了。配置好参数之后，运行的指令为：
$ ../SPONGE -mdin minimize.txt
就可以获得相应的输出。
其他类型模拟
最常见的就是控温，那么主要就是设定
mode=NVT
，例如这是一个简单的
nvt.txt
，对应SPONGE的mdin输入文件：
case1 MD simulation
mode = NVT
default_in_file_prefix = protein/case1
pbc=0
cutoff=999
dt = 1e-3
step_limit = 50000
write_information_interval = 5000
thermostat = middle_langevin
middle_langevin_gamma = 10
rst = nvt_restart
coordinate_in_file = restart_coordinate.txt
这里起始坐标直接使用能量极小化之后的结果，并将NVT的最终坐标保存到
nvt_restart_coordinate.txt
文件中。其他如NPT模式的配置，可以参考
这篇博客
中的介绍。
增强采样
在CudaSPONGE v1.4的版本中，增强采样方法的定义形式如下
meta.txt
：
case1 MD simulation
mode = NVT
default_in_file_prefix = protein/case1
pbc=0
cutoff=999
dt = 1e-3
step_limit = 50000
write_information_interval = 5000
target_temperature = 300.0
thermostat = middle_langevin
middle_langevin_gamma = 10
rst = meta_restart
coordinate_in_file = nvt_restart_coordinate.txt
cv_in_file = cv.txt
dont_check_input = 1
其中额外包含了一个CV的定义文件
cv.txt
，内容如下：
print
{
CV = torsion
}
torsion
{
CV_type = dihedral
atom = 1 3 12 13
}
meta1d
{
CV = torsion
dCV = 0.06
CV_minimal = -3.1416
CV_maximum = 3.1416
CV_period = 6.2832
welltemp_factor = 50
height = 1
sigma = 0.3
}
一样的运行方法，可以看到输出结果如下：
$ ../SPONGE -mdin meta.txt
SPONGE Version:
v1.4 2024-01-01
Sub-package:
SPONGE, for normal molecular dynamics simulations
Citation:
Huang, Y. - P., Xia, Y., Yang, L., Wei, J., Yang, Y.I.and Gao, Y.Q. (2022), SPONGE: A GPU - Accelerated Molecular Dynamics Package with Enhanced Sampling and AI - Driven Algorithms.Chin.J.Chem., 40 : 160 - 168. https ://doi.org/10.1002/cjoc.202100456
MD TASK NAME:
case1 MD simulation
START INITIALIZING CONTROLLER
Start initializing CUDA
Compiled by CUDA 11.6
1 device found:
Device 0:
Name: NVIDIA GeForce RTX 3080 Ti Laptop GPU
Memory: 16.0 GB
Compute Capability: 86
Set Device 0
End initializing CUDA
structure last modify date is 20231219
END INITIALIZING CONTROLLER
START INITIALIZING CV CONTROLLER:
1 CV defined
0 cv virtual atoms
END INITIALIZING CV CONTROLLER
START INITIALIZING MD CORE:
Mode set to NVT
dt set to 0.001000 ps
Start reading mass:
End reading mass
Start reading charge:
End reading charge
Start reading coordinate_in_file:
atom_numbers is 57
system start_time is 50.000000
box_length is
x: 999.000000
y: 999.000000
z: 999.000000
End reading coordinate_in_file
Velocity is set to zero as default
skin set to 2.00 Angstrom
cutoff set to 999.00 Angstrom
Start reading excluded list:
excluded list total length is 290
End reading excluded list
Start reading residue list:
residue_numbers is 4
End reading residue list
structure last modify date is 20211105
END INITIALIZING MD CORE
START INITIALIZING MIDDLE LANGEVIN DYNAMICS:
atom_numbers is 57
target temperature is 300.00 K
friction coefficient is 10.00 ps^-1
random seed is 1476805525
structure last modify date is 20210826
END INITIALIZING MIDDLE LANGEVIN DYNAMICS
START INITIALIZING LENNADR JONES INFORMATION:
atom_numbers is 57
atom_LJ_type_number is 8
structure last modify date is 20220601
END INITIALIZING LENNADR JONES INFORMATION
START INITIALIZING COULOMB INFORMATION:
structure last modify date is 20220603
END INITIALIZING COULOMB INFORMATION
START INITIALIZING NB14 (nb14_in_file):
non-bond 14 numbers is 135
structure last modify date is 20211222
END INITIALIZING NB14
LISTED FORCES IS NOT INITIALIZED
START INITIALIZING BOND (bond_in_file):
bond_numbers is 56
structure last modify date is 20210830
END INITIALIZING BOND
START INITIALIZING BOND SOFT:
END INITIALIZING SOFT BOND
START INITIALIZING ANGLE (angle_in_file):
angle_numbers is 99
structure last modify date is 20210830
END INITIALIZING ANGLE
UREY BRADLEY IS NOT INITIALIZED
START INITIALIZING DIHEDRAL (dihedral_in_file):
dihedral_numbers is 137
structure last modify date is 20210830
END INITIALIZING DIHEDRAL
IMPROPER DIHEDRAL IS NOT INITIALIZED
START INITIALIZING CMAP:
CMAP IS NOT INITIALIZED
START INITIALIZING HARD WALL:
END INITIALIZING HARD WALL
SOFT WALLS ARE NOT INITIALIZED
RESTRAIN IS NOT INITIALIZED
START INITIALIZING RESTRAIN CV:
0 CV(s) found for restrain
RESTRAIN CV IS NOT INITIALIZED
START INITIALIZING STEER CV:
0 CV(s) found for steer
STEER CV IS NOT INITIALIZED
START INITIALIZING META1D:
1 CV(s) found for meta1d
CV 0: torsion
reading 4 atom(s) for torsion
atom 0: 1
atom 1: 3
atom 2: 12
atom 3: 13
type of 'torsion' is 'dihedral'
reading 1 CV_period(s) for meta1d
CV_period 0: 6.283200
reading 1 CV_minimal(s) for meta1d
CV_minimal 0: -3.141600
reading 1 CV_maximum(s) for meta1d
CV_maximum 0: 3.141600
reading 1 dCV(s) for meta1d
dCV 0: 0.060000
reading 1 height(s) for meta1d
height 0: 1.000000
reading 1 sigma(s) for meta1d
sigma 0: 0.300000
reading 1 welltemp_factor(s) for meta1d
welltemp_factor 0: 50.000000
Potential update interval is set to write_information_interval by default
potential output file: meta1d_potential.txt
END INITIALIZING META1D
VIRTUAL ATOM IS NOT INITIALIZED
START INITIALIZING CV PRINTER:
1 CV(s) found for print
CV 0: torsion
type of 'torsion' is 'dihedral'
END INITIALIZING CV PRINTER
------------------------------------------------------------------------------------------------------------
step = 5000, time = 55.000, temperature = 391.02,
potential = -187.55, LJ = -6.25, Coulomb = -308.21,
nb14_LJ = 7.49, nb14_EE = 23.77, bond = 19.29,
angle = 31.16, dihedral = 43.88, meta1d = 1.32,
torsion = -2.3809,
------------------------------------------------------------------------------------------------------------
step = 10000, time = 60.000, temperature = 298.28,
potential = -183.35, LJ = -5.40, Coulomb = -316.07,
nb14_LJ = 9.65, nb14_EE = 29.10, bond = 19.95,
angle = 33.31, dihedral = 43.66, meta1d = 2.45,
torsion = -2.5452,
------------------------------------------------------------------------------------------------------------
step = 15000, time = 65.000, temperature = 433.99,
potential = -188.78, LJ = -4.70, Coulomb = -316.29,
nb14_LJ = 8.71, nb14_EE = 23.72, bond = 21.29,
angle = 26.82, dihedral = 47.90, meta1d = 3.77,
torsion = -2.4958,
------------------------------------------------------------------------------------------------------------
step = 20000, time = 70.000, temperature = 249.71,
potential = -183.19, LJ = -5.34, Coulomb = -329.13,
nb14_LJ = 9.73, nb14_EE = 31.84, bond = 22.68,
angle = 34.74, dihedral = 50.28, meta1d = 2.01,
torsion = -1.9129,
------------------------------------------------------------------------------------------------------------
step = 25000, time = 75.000, temperature = 355.19,
potential = -190.72, LJ = -7.80, Coulomb = -314.26,
nb14_LJ = 8.21, nb14_EE = 23.10, bond = 19.06,
angle = 29.59, dihedral = 48.39, meta1d = 3.01,
torsion = -1.8429,
------------------------------------------------------------------------------------------------------------
step = 30000, time = 80.000, temperature = 407.06,
potential = -181.22, LJ = 0.79, Coulomb = -293.82,
nb14_LJ = 6.62, nb14_EE = 5.15, bond = 24.57,
angle = 32.20, dihedral = 41.94, meta1d = 1.32,
torsion = 0.4504,
------------------------------------------------------------------------------------------------------------
step = 35000, time = 85.000, temperature = 203.30,
potential = -179.47, LJ = 0.97, Coulomb = -298.49,
nb14_LJ = 8.28, nb14_EE = 4.97, bond = 27.75,
angle = 39.17, dihedral = 35.27, meta1d = 2.61,
torsion = 0.4398,
------------------------------------------------------------------------------------------------------------
step = 40000, time = 90.000, temperature = 310.20,
potential = -190.12, LJ = -3.52, Coulomb = -296.07,
nb14_LJ = 9.64, nb14_EE = 13.64, bond = 16.37,
angle = 28.68, dihedral = 39.10, meta1d = 2.03,
torsion = -0.0447,
------------------------------------------------------------------------------------------------------------
step = 45000, time = 95.000, temperature = 408.99,
potential = -190.56, LJ = -2.71, Coulomb = -296.55,
nb14_LJ = 8.19, nb14_EE = 10.34, bond = 19.28,
angle = 30.85, dihedral = 36.49, meta1d = 3.57,
torsion = 0.0334,
------------------------------------------------------------------------------------------------------------
step = 50000, time = 100.000, temperature = 462.33,
potential = -189.09, LJ = -0.75, Coulomb = -293.79,
nb14_LJ = 9.71, nb14_EE = 6.49, bond = 18.99,
angle = 27.54, dihedral = 38.08, meta1d = 4.63,
torsion = -0.0077,
------------------------------------------------------------------------------------------------------------
Core Run Wall Time: 13.704983 seconds
Core Run Speed: 315.220093 ns/day
End Pause
总结概要
本文简单介绍了一下CudaSPONGE高性能分子动力学模拟软件，其基于原生的CUDA C开发，具有极高的模拟效率。结合前处理工具Xponge用于生成和处理输入文件，可以很好的兼容目前常用的很多力场形式。
版权声明
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https://www.cnblogs.com/dechinphy/p/cudasponge.html
作者ID：DechinPhy
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https://www.cnblogs.com/dechinphy/
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