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

[Mark Abraham]

Hi,

On Wed, Jun 21, 2017 at 3:24 AM Adarsh V. K. <adarsh_p130085bt at nitc.ac.in>
wrote:

> Dear all,
>
> *I used following command to extend a NPT simulation*
>
> 1) gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
>             gmx mdrun -deffnm tpxout -cpi npt.cpt -v
>
> but the analysis " gmx energy -f  *tpxout*.edr -o pressure.xvg " shows only
> the extended part; How to append the extend part to previous cpt


trjcat and eneconv


> and
> continue to production MD ?
>

You don't want to append all your equilibration data and then your
production data. You're going to discard your equilibration period before
you analyse the data you produce...

-------
> *Now to do a final MD simulation what command I should use?*
>
> 2) 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
>
> 3) 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
>

These are identical except for the grompp -t, which controls what
configuration is written to the .tpr. Choose the one that makes sense for
the point from which you are trying to start.

Mark

*no need to combine; just use the third command to continue to MD
> simulation?*
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