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

[Mark Abraham]

Hi

On Wed, May 31, 2017 at 2:50 AM Adarsh V. K. <adarsh_p130085bt at nitc.ac.in>
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
>

If the npt run was long enough, you'll have both npt.cpt and npt_prev.cpt
(as a backup). Use the one that was written later.


> *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
>

Give to grompp -t the cpt file from the end of the run you're intending to
continue.

Using npt.cpt would be particularly strange if you used npt_prev.cpt to
extend the npt run and write tpxout, because now you've thrown away the
extended component.

Mark


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