[gmx-users] gromacs error in vacuum preparation simulation

Justin Lemkul jalemkul at vt.edu
Mon Mar 11 21:11:43 CET 2019

On 3/11/19 3:20 PM, Mario Andres Rodriguez Pineda wrote:
> Hi everybody
> I want to do one dynamic simulation of one protein
> i'm try to minimize the protein in vacum before the simulation runing but
> gromacs send me this error:
> -------------------------------------------------------
> Program:     gmx grompp, version 2018.6
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991)
> Fatal error:
> There was 1 error in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> this is the command that i use for minimization in vacum.
> gmx_mpi grompp -f vacuum.mdp -c cbd212_box.gro -p topol.top -o
> cbd212_vac.tpr -maxwarn 1

Run grompp interactively if you want to see the actual error. It may 
also be printed to a log file from your queuing system. Also, never use 



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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