output togmx_mpi -quiet -version: :-) GROMACS - gmx_mpi, 2023 (-:Executable: /home/apeng/.local/gromacs_2023/bin/gmx_mpiData prefix: /home/apeng/.local/gromacs_2023Working dir: /home/apeng/research/dmref/experiments/ap23-06/pmmaph/flow-runs/debug-runsCommand line:gmx_mpi -quiet -...
[INFO ] Starting gmx_MMPBSA v1.5.0.2 [INFO ] Command-line mpirun -np 10 gmx_MMPBSA MPI -O -i mmpbsa1.in -cs md_2020.tpr -ci md.ndx -cg 17 18 -ct md_C2.xtc -cp complex.top [INFO ] Checking external programs... [INFO ] cpptraj found!Using /home/jq/anaconda3/envs/gmxMM...
gmx_MMPBSAlike MMPBSA.py is trivially parallelized. That is, the path is divided into as many chunks as the CPU is provided. Unless you explicitly require theMPIcapability of the AmberTools programs, it is not required forgmx_MMPBSA. According to my tests (using the same command line), ...
And then, run my simulation via gmx mdrun. Here is my command: gmx mdrun-v-deffnmProdutcion-sProduction.tpr-ntomp12-pinon-ntmpi1-updategpu-bondedgpu An "Assertion failed" error occurs. :-)GROMACS - gmx mdrun, 2023.1(-:Executable: /home/yangzichen/Software/GMX-2023.1/bin/gmxData prefix...
cmake -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_BINARY_SUFFIX=_mpi A summary of the output given by this command is: CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE ...
although I have installed gromacs 4.6.1 with float double and mpi options but they were all without GPU options. SO when I started installing 4.6.1 version with GPU I ran into problems. So I figured it has got to have sth to do with the GPU! I don't know what environment variables ...
AMBER tpr,pdb ndx xtc,trr,pdb optional Optional Only if not top defined CHARMM tpr,pdb ndx xtc,trr,pdb Always Optional No Usage Running # mmpbsa.in输入文件的创建见下文 mpirun -np 2 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 1 13 -ct md.xtc -cp topol.top...
mpiContextManager_(std::make_unique<MpiContextManager>()), simulationContext_(simulationContext), logFilePtr_(std::move(fplog)), multiSim_(multiSim) {GMX_ASSERT(context_,"SessionImpl invariant implies valid ContextImpl handle.");GMX_ASSERT(mpiContextManager_,"SessionImpl invariant implies valid Mpi...
[DEBUG ] MPI : /home/qms/miniconda3/envs/gmxMMPBSA/bin/mpirun [DEBUG ] ParmEd : 3.4.4 [DEBUG ] OS PLATFORM : Linux-6.5.0-18-generic-x86_64-with-glibc2.35 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION :#18~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 7 11:40:03 UTC 2 ...
59 module show gromacs 然后看prepend-path里的bin里面的gromacs叫什么 大概率叫gmx_mpi 非常感谢。