GROMACS version: 2022.1 and 2020
GROMACS modification: Yes/No
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Hello, I am trying to simulate Lipid based vesicle in GROMACS on Frontera super-computer. The following command I am using to run the simulation. But I am getting error messages. Since I am new I don’t understand the error message perfectly. Is this a problem with charmm gui generated file or problem in my run_script. I am trying to run the simulation using README file generated from charmm. I combined that README file and Frontera job script together but my job get cancelled. After that I am using step by step command from README file. My another question is why I cannot use the all command line from README file at once?
Thank you
#!/bin/bash
#SBATCH -J myjob # job name
#SBATCH -e myjob.%j.err # error file name
#SBATCH -o myjob.%j.out # output file name
#SBATCH -N 10 # request 10 nodes
#SBATCH -n 54 # request 4x56=224 MPI tasks
#SBATCH -p normal # designate queue
#SBATCH -t 24:00:00 # designate max run time
module load gromacs/2022.1
export OMP_NUM_THREADS=1 # 1 OMP thread per MPI task
gmx grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_charmm2gmx.pdb -p system.top -r lipidtail_posres.pdb -n index.ndx
ibrun gmx_mpi mdrun -s topol.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log
README file:
#!/bin/bash
Generated by CHARMM-GUI (http://www.charmm-gui.org)
1) Use Gromacs 5.1 or newer to run these simulations
2) DVESICLE_LIPIDTAIL_R in the mdp files defines the radius of three water pores (along X, Y and Z axis)
in the vesicle to let the lipids exchange between the inner and outer layer
3) Make sure the vesicle is equilibrated well before close the water pore
Minimization
setenv GMX_MAXCONSTRWARN -1
step6.0 - soft-core minimization
gmx grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_charmm2gmx.pdb -p system.top -r lipidtail_posres.pdb -n index.ndx
gmx mdrun -deffnm step6.0_minimization
step6.1
gmx grompp -f step6.1_minimization.mdp -o step6.1_minimization.tpr -c step6.0_minimization.gro -p system.top -r lipidtail_posres.pdb -n index.ndx
gmx mdrun -deffnm step6.1_minimization
unsetenv GMX_MAXCONSTRWARN
Equilibration
set cnt = 2
set cntmax = 6
while ( {cnt} <= {cntmax} )
@ pcnt = ${cnt} - 1
if (cnt == 2) then
gmx grompp -f step6.{cnt}_equilibration.mdp -o step6.{cnt}_equilibration.tpr -c step6.{pcnt}_minimization.gro -p system.top -r lipidtail_pos$
else
gmx grompp -f step6.{cnt}_equilibration.mdp -o step6.{cnt}_equilibration.tpr -c step6.{pcnt}_equilibration.gro -p system.top -r lipidtail_po
endif
gmx mdrun -deffnm step6.${cnt}_equilibration
@ cnt += 1
end
Production
gmx grompp -f step7_production.mdp -o step7_production.tpr -c step6.6_equilibration.gro -p system.top -r lipidtail_posres.pdb -n index.ndx
gmx mdrun -deffnm step7_production
Error message:
Error in user input:
Invalid command-line options
Program: gmx mdrun, version 2022.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function: void gmx::CommandLineParser::parse(int *, char **)
MPI rank: 46 (out of 54)
Error in user input:
Program: gmx mdrun, version 2022.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function: void gmx::CommandLineParser::parse(int *, char **)
MPI rank: 40 (out of 54)
Error in user input:
Program: gmx mdrun, version 2022.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Error in user input:
Invalid command-line options
Program: gmx mdrun, version 2022.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function: void gmx::CommandLineParser::parse(int *, char **)
MPI rank: 51 (out of 54)
Error in user input:
Program: gmx mdrun, version 2022.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function: void gmx::CommandLineParser::parse(int *, char **)
MPI rank: 32 (out of 54)