CHARMM-Gui Script

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1

GROMACS version:2020.2
GROMACS modification: No
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Dear All,
I am naive and learning Gromacs simulation. I prepared inputs from CHARMM-Gui. I got the following script from charmm-gui. It basically runs one cycle of minimization and equilibration. finally 10 cycle of md production, each for 1ns. as i understood, the new cycle takes input from previous cycle. so is it considered 10ns simulation at the end of 10th cycle? Because each cycle continues from previous cycle. if answer is yes, then how can i get .xtc or .tpr files for 10 ns to plot rmsd? and if answer is no, then whats the purpose of running 10 production cycle. Thank you
Script is here-

#!/bin/cshs

Generated by CHARMM-GUI (http://www.charmm-gui.org)

This folder contains GROMACS formatted CHARMM36 force fields, a pre-optimized PDB structure, and GROMACS inputs.

All input files were optimized for GROMACS 2019.2 or above, so lower version of GROMACS can cause some errors.

We adopted the Verlet cut-off scheme for all minimization, equilibration, and production steps because it is

faster and more accurate than the group scheme. If you have a trouble with a performance of Verlet scheme while

running parallelized simulation, you should check if you are using appropriate command line.

For MPI parallelizing, we recommand following command:

mpirun -np $NUM_CPU gmx mdrun -ntomp 1

Minimization

In the case that there is a problem during minimization using a single precision of GROMACS, please try to use

a double precision of GROMACS only for the minimization step.

step4.0

gmx grompp -f step4.0_minimization.mdp -o step4.0_minimization.tpr -c step3_input.gro -r step3_input.gro -p topol.top -maxwarn 1
gmx_d mdrun -v -deffnm step4.0_minimization

Equilibration

step4.1

gmx grompp -f step4.1_equilibration.mdp -o step4.1_equilibration.tpr -c step4.0_minimization.gro -r step3_input.gro -p topol.top
gmx mdrun -v -deffnm step4.1_equilibration

Production

set cnt = 1
set cntmax = 10

while ( {cnt} <= {cntmax} )
if ( {cnt} == 1 ) then gmx grompp -f step5_production.mdp -o step5_{cnt}.tpr -c step4.1_equilibration.gro -p topol.top
gmx mdrun -v -deffnm step5_{cnt} else @ pcnt = {cnt} - 1
gmx grompp -f step5_production.mdp -o step5_{cnt}.tpr -c step5_{pcnt}.gro -t step5_{pcnt}.cpt -p topol.top gmx mdrun -v -deffnm step5_{cnt}
endif
@ cnt += 1
end

2

Missing superscript or subscript argument==$

3

Yes.

Use trjcat to concatenate trajectories. Use any .tpr file for analysis that makes sense for what you want to compute (e.g. if you want RMSD relative to the crystal structure, use the .tpr file from energy minimization, which has the original coordinates; if you want RMSD relative to the equilibrated coordinates, use the first production .tpr as the reference).

4

Thank you Dr Jalekul for quick response.

Best
Veeru

5

Hi.
I think you can help me with my last topic.
My question is some thing about increasing radius of carbon and using Charmm gui…