GROMACS version: 2021.3
GROMACS modification: Yes/No
I am facing problem while submitting my job for energy minimization. I am following This tutorial. and using HPC for simulation. I am a beginner please help me.
Could you provide details on what the problem is?
Program: gmx mdrun, version 2021.3
Source file: src/gromacs/options/options.cpp (line 179)
Function: void gmx::internal::OptionSectionImpl::finish()
MPI rank: 70 (out of 72)
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file ‘topol’ does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
MPI_ABORT was invoked on rank 2 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.
[kuhpccn2:25498] 71 more processes have sent help message help-mpi-api.txt / mpi-abort
[kuhpccn2:25498] Set MCA parameter “orte_base_help_aggregate” to 0 to see all help / error messages
I got this message.
It seems one of the commands you entered requires a .tpr file to be specified with the -s flag, you’ll need to figure out which command is throwing the error and which .tpr is required
Fatal error:
number of coordinates in coordinate file (box_sol.gro, 50355)
does not match topology (topol.top, 50356)
Getting this error while adding ions to the system. Have checked the .itp file along with topol.top.
That’s alright.
This time I’ve run completely fresh. And used AMBER 99SB force field.
As the error states, it seems the topology files list one extra atom not found in the coordinate file. You’ll have to go through the atoms listed for each residue in the .top/.itp files and compare it with the same residue type in the .gro file to figure out where the error happened.