GROMACS version: 2021.4-plumed-2.8.0
GROMACS modification: Yes/No
Here post your question
I want to perform steered molecular dynamics in gromacs with plumed. I have patched plumed with gromacs. But I don’t know how to run plumed now. I mean I tried gmx mdrun -plumed plumed.dat, with the script written in plumed.dat, but got an error. How should I proceed? I mean I have an equilibrated system named nvt.gro wherein I want to run the smd by following the distance between the COM of two particles and measuring the corresponding work done. I got an error stating that file with extension .tpr was not found. How should I create such a file?
Please provide actual error messages, directly copied and pasted from the terminal.
If the issue is with PLUMED, please use their help forum.
:-) GROMACS - gmx mdrun, 2021.4-plumed-2.8.0 (-:
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GROMACS: gmx mdrun, version 2021.4-plumed-2.8.0
Executable: /home/niladri/gromacs21-4-mpi-plumed/bin/gmx_mpi
Data prefix: /home/niladri/gromacs21-4-mpi-plumed
Working dir: /home/niladri/Gourav/SMD_calc/25_percent/dodecane_equilibration
Command line:
gmx_mpi mdrun -v -deffnm md -ntmpi 0 -ntomp 32 -pin on -pinoffset 0 -plumed plumed.dat
Back Off! I just backed up md.log to ./#md.log.2#
Reading file md.tpr, VERSION 2021.4 (single precision)
Changing nstlist from 10 to 100, rlist from 1.2 to 1.2
Using 1 MPI process
Using 32 OpenMP threads
Back Off! I just backed up md.trr to ./#md.trr.2#
Back Off! I just backed up md.edr to ./#md.edr.2#
starting mdrun ‘SIL in water’
1000000 steps, 1000.0 ps.
[raman:167854] *** Process received signal ***
[raman:167854] Signal: Segmentation fault (11)
[raman:167854] Signal code: Address not mapped (1)
[raman:167854] Failing at address: (nil)
[raman:167854] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x430c0)[0x7f4198a8c0c0]
[raman:167854] [ 1] /opt/plumed/lib/libplumedKernel.so(ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT+0x9f)[0x7f4197ff4f0f]
[raman:167854] [ 2] /opt/plumed/lib/libplumedKernel.so(_ZNK4PLMD3PDB13getChainNamesERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE+0x264)[0x7f41984970b4]
[raman:167854] [ 3] /opt/plumed/lib/libplumedKernel.so(_ZN4PLMD14GenericMolInfoC1ERKNS_13ActionOptionsE+0x852)[0x7f4198189c12]
[raman:167854] [ 4] /opt/plumed/lib/libplumedKernel.so(+0x494757)[0x7f41981f4757]
[raman:167854] [ 5] /opt/plumed/lib/libplumedKernel.so(_ZN4PLMD14ActionRegister6createERKNS_13ActionOptionsE+0x614)[0x7f4198154774]
[raman:167854] [ 6] /opt/plumed/lib/libplumedKernel.so(_ZN4PLMD10PlumedMain14readInputWordsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE+0x280)[0x7f41981a0880]
[raman:167854] [ 7] /opt/plumed/lib/libplumedKernel.so(_ZN4PLMD10PlumedMain13readInputFileERNS_5IFileE+0x54)[0x7f41981a0ce4]
[raman:167854] [ 8] /opt/plumed/lib/libplumedKernel.so(_ZN4PLMD10PlumedMain13readInputFileERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0xa3)[0x7f41981a3ee3]
[raman:167854] [ 9] /opt/plumed/lib/libplumedKernel.so(_ZN4PLMD10PlumedMain4initEv+0x124a)[0x7f41981a52ea]
[raman:167854] [10] /opt/plumed/lib/libplumedKernel.so(_ZN4PLMD10PlumedMain3cmdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrE+0x1bb5)[0x7f41981a7415]
[raman:167854] [11] /opt/plumed/lib/libplumedKernel.so(+0x44b806)[0x7f41981ab806]
[raman:167854] [12] /home/niladri/gromacs21-4-mpi-plumed/lib/libgromacs_mpi.so.6(_ZN3gmx15LegacySimulator5do_mdEv+0x1c65)[0x7f4199a27e55]
[raman:167854] [13] /home/niladri/gromacs21-4-mpi-plumed/lib/libgromacs_mpi.so.6(_ZN3gmx15LegacySimulator3runEv+0x72)[0x7f4199a25f62]
[raman:167854] [14] /home/niladri/gromacs21-4-mpi-plumed/lib/libgromacs_mpi.so.6(_ZN3gmx8Mdrunner8mdrunnerEv+0x61e9)[0x7f4199a603e9]
[raman:167854] [15] gmx_mpi(+0xb75a)[0x56481b63275a]
[raman:167854] [16] gmx_mpi(+0xb902)[0x56481b632902]
[raman:167854] [17] /home/niladri/gromacs21-4-mpi-plumed/lib/libgromacs_mpi.so.6(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x280)[0x7f419939a600]
[raman:167854] [18] gmx_mpi(+0x7eb0)[0x56481b62eeb0]
[raman:167854] [19] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f4198a6d0b3]
[raman:167854] [20] gmx_mpi(+0x7f3e)[0x56481b62ef3e]
[raman:167854] *** End of error message ***
Segmentation fault (core dumped)
I want to run SMD here with to determine the work done when the distance between the COM of two particles is increased. For this I have already equilibrated the system (NVT equilibration was done). But when I ran the command gmx_mpi mdrun -plumed plumed.dat (with the moleinfo command = nvt.gro, in order to read the nvt.gro file obtained from NVT equilibration) I got an error as mdrun requires .tpr file. So I was not sure, which .tpr file it requires. So I created another tpr file for a simple 1ns production run (named md.tpr) but when used with plumed, I got a segmentation fault.
An mdrun process always requires instructions for doing the dynamics, hence why you need a .tpr file, and its settings must be sensible for the type of simulation you’re running. Regardless, this all looks like some kind of PLUMED failure. If the md.tpr file runs without PLUMED options, you can confirm that. And if it is a PLUMED problem, please inquire on their forums.
ok. But I have one question here. If I want to run an SMD calculation, what should be the input parameters for the corresponding .mdp file? I mean can I run SMD without plumed in gromacs?
One possible example: Umbrella Sampling