# Lipid vesicle(CHARMM Gui files) simulation in GROMACS

**URL:** <https://gromacs.bioexcel.eu/t/lipid-vesicle-charmm-gui-files-simulation-in-gromacs/7886>\
**Category:** User discussions\
**Created:** [December 18, 2023, 11:52pm UTC](https://gromacs.bioexcel.eu/t/lipid-vesicle-charmm-gui-files-simulation-in-gromacs/7886 "2023-12-18T23:52:01Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![fhaque](https://avatars.discourse-cdn.com/v4/letter/f/48db29/32.png) [@fhaque](https://gromacs.bioexcel.eu/u/fhaque)\
**Post date:** [December 18, 2023, 11:52pm UTC](https://gromacs.bioexcel.eu/t/lipid-vesicle-charmm-gui-files-simulation-in-gromacs/7886/1 "2023-12-18T23:52:01Z")

</div>

GROMACS version: 2022.1 and 2020  
GROMACS modification: Yes/No  
Here post your question  
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](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)