[gmx-users] Unable to run gmx_mpi genion non-interactively

[Chenyu Liu]

Hi Sarah,
Here is part of my .pbs file for submitting job to server:
gmx_mpi genion -s ions.tpr -o xx_solv_ions.gro -p topol.top -pname NA
-nname CL -neutral <<EOF
SOL
EOF

(Reference:
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts)

I hope this will help you.

Chenyu Liu


On Thu, Oct 3, 2019 at 4:53 PM Sarah Lucas <u1264169 at utah.edu> wrote:

> Dear GMX experts,
>
> I am trying to model a protein building its ligand but am having trouble
> generating the ions before I proceed with the energy minimization.  I have
> been following the Protein-Ligand tutorial and able to make the commands
> run non-interactively using MPI.  I tried following
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts to
> no avail. Currently, I am using Gromacs/2016.4.d with intel/2018.5.274 and
> impi same version. I tried using Gromacs/2019.1. My other option is version
> 5.0.4 Does anyone have a suggestion how to run genion non-interactively?
> Below are the line from my slurm file and the outputs it generated.
>
> SLURM file command:
> mpirun -np $MPI_NTASKS gmx_mpi_d genion -s wt_model_ions.tpr -o
> wt_model_solv.ions.gro -p topol_model.top -nname CL -nn 3 < sol.txt
>
> sol.txt contains
> 15
>
> Error File:
> Fatal error:
> Group     0 (         System) has 105532 elements
> Group     1 (        Protein) has  6216 elements
> Group     2 (      Protein-H) has  3110 elements
> Group     3 (        C-alpha) has   399 elements
> Group     4 (       Backbone) has  1197 elements
> Group     5 (      MainChain) has  1595 elements
> Group     6 (   MainChain+Cb) has  1963 elements
> Group     7 (    MainChain+H) has  1966 elements
> Group     8 (      SideChain) has  4250 elements
> Group     9 (    SideChain-H) has  1515 elements
> Group    10 (    Prot-Masses) has  6216 elements
> Group    11 (    non-Protein) has 99316 elements
> Group    12 (          Other) has    49 elements
> Group    13 (            LIG) has    49 elements
> Group    14 (          Water) has 99267 elements
> Group    15 (            SOL) has 99267 elements
> Group    16 (      non-Water) has  6265 elements
> Select a group:
> -------------------------------------------------------
> Program:     gmx genion, version 2016.4
> Source file: src/gromacs/topology/index.cpp (line 930)
> MPI rank:    3 (out of 16)
> Fatal error:
> Cannot read from input
>
> Output File:
> Will try to add 0 NA ions and 3 CL ions.
> Select a continuous group of solvent molecules
>
> Thank you very much for your assistance,
> Sarah
>
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