[gmx-users] query regarding state.cpt file

[sudha bhagwati]

Dear Dr. Justin,
Thank you so much for the reply.

Regards
~
Sudha

On Thu, Jan 17, 2019 at 3:41 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
>
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-- 
Thanks & regards
~
Sudha Bhagwati