[gmx-users] query regarding state.cpt file

[Justin Lemkul]

On 1/15/19 11:29 PM, sudha bhagwati wrote:
>   MD_output.tar.gz
> <https://drive.google.com/file/d/1aJewpvBzeeH4C6o53nCl2qaPTCFDaDeD/view?usp=drive_web>
> Greetings Sir/Madam
>
> I am running MD simulation using commands listed below-
> _______________________________________________________________________________________________________________________________________
> gmx pdb2gmx -ignh -f protein.pdb
> gmx editconf -f ligand.pdb -o ligand.gro
>
> gmx editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
> gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>
> gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
> gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL
> -neutral
>
> gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr
> gmx mdrun -v -deffnm em
>
> gmx make_ndx -f em.gro -o index.ndx
>
> gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
>
> gmx mdrun -v -deffnm nvt
>
> gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o
> npt.tpr
>
> gmx mdrun -v -deffnm npt
>
> gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
> md_0_20.tpr
>
> gmx mdrun -v -deffnm md_0_20
> _____________________________________________________________________________________________________________________________________
>
> I have attached the tar file for generated output files from complete
> gromacs run.

The mailing list does not accept attachments.

> I am not an expert user of gromacs. So which file I can use as state.cpt
> and what is the command to rerun my stopped MD run?

You asked for files to be called md_0_20 as the prefix, so you will have 
md_0_20.cpt as the final checkpoint file.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================