[gmx-users] gromacs error in vacuum preparation simulation

Mario Andres Rodriguez Pineda mandres at iq.usp.br
Mon Mar 11 20:21:07 CET 2019

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

I can't find the solution for this problem.

Thanks for your help
*Estudiante Doctorado en Biotecnología*


*Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas *
*Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091

More information about the gromacs.org_gmx-users mailing list