[gmx-users] How to perform final MD simulation after extending a NPT simulation

[Justin Lemkul]

On 5/30/17 8:50 PM, Adarsh V. K. wrote:
> Dear all,
> 
> *I used following command to extend a NPT simulation*
> 
> gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
> gmx mdrun -deffnm tpxout -cpi npt_prev.cpt -v
> 
> *Now to do final MD simulation what command I should use?*
> 
> gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
> md_0_1.tpr
> gmx mdrun -deffnm md_0_1 -v
> 
> or
> 
> gmx grompp -f md.mdp -c npt.gro -t tpxout.cpt -p topol.top -n index.ndx -o
> md_0_1.tpr
> gmx mdrun -deffnm md_0_1 -v
> 

I suggest you use gmx check to investigate the contents and differences between 
the checkpoint files.  If "npt" is the first part of the run, and "tpxout" is 
the second part, and you want to continue from the second part...

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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