Problem with gromacs script generetated with charmm-gui

User discussions
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1

Hi all,

I generated a protein-membrane system using CHARMM-GUI. For production, I am using the following loop script provided by CHARMM-GUI (slightly adapted):

# Define variables
init="../step5_input"
rest_prefix="../step5_input"
mini_prefix="../minimization/step6.0_minimization"
equi_prefix="../equilibration/step6.%d_equilibration"
prod_prefix="step7_production"
prod_step="step7"

# Production loop
cnt=1
cntmax=10

while [ $cnt -le $cntmax ]; do
    pcnt=$((cnt - 1))
    istep="${prod_step}_${cnt}"
    pstep="${prod_step}_${pcnt}"

    if [ $cnt -eq 1 ]; then
        printf -v pstep "$equi_prefix" 6
        gmx grompp -f "../${prod_prefix}.mdp" -o "${istep}.tpr" -c "${pstep}.gro" -p ../topol.top -n ../index.ndx
    else
        gmx grompp -f "../${prod_prefix}.mdp" -o "${istep}.tpr" -c "${pstep}.gro" -t "${pstep}.cpt" -p ../topol.top -n ../index.ndx
    fi

    gmx mdrun -v -deffnm "${istep}" -ntmpi 1 -ntomp ${SLURM_CPUS_PER_TASK:-1} -bonded gpu -pme gpu -pin on -pinstride 1 -maxh 0.33 -cpt 20 
    cnt=$((cnt + 1))
done

However, when starting the second production step, I get the following error, after the first iteration:

Program:     gmx grompp, version 2022.3
Error in user input:
Invalid command-line options
  In command-line option -c
    File 'step7_1.gro' does not exist or is not accessible.
    The file could not be opened.
      Reason: No such file or directory

It seems like the .gro file from the previous step is not being generated. Could it be that I’m missing a flag or option in mdrun to write the output .gro file? Or is something wrong with the naming logic?

Any help would be appreciated!

Thanks in advance.

2

Mostly likely, it means a previous step failed. Check all logs and output files.

3

@jalemkul thanks for your reply!

I have checking the log files and the 2 only notes that I found were the following ones

Executable:   /opt/ohpc/pub/apps/gnu9/openmpi4/gromacs/2022.3/bin/gmx
Data prefix:  /opt/ohpc/pub/apps/gnu9/openmpi4/gromacs/2022.3
Working dir:  /masc_shared/NTSR1_gromacs_2022/prod1
Command line:
  gmx grompp -f ../step7_production.mdp -o step7_1.tpr -c ../equilibration/step6.6_equilibration.gro -p ../topol.top -n ../index.ndx

Generating 1-4 interactions: fudge = 1

NOTE 1 [file topol.top, line 30]:
  The bond in molecule-type POPC between atoms 31 C21 and 32 O22 has an
  estimated oscillational period of 2.1e-02 ps, which is less than 10 times
  the time step of 4.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group SOLU is 14969.88
Number of degrees of freedom in T-Coupling group MEMB is 363837.12
Number of degrees of freedom in T-Coupling group SOLV is 924972.00

NOTE 2 [file ../step7_production.mdp]:




Step 132350: Run time exceeded 0.327 hours, will terminate the run within 50 steps

Could be the reason of the error?

step7_1.log (101.9 KB)

mdout.mdp (10.4 KB)

4

Yes, if the job did not complete, you will not get the final coordinates in step7_1.gro.