[gmx-users] md continuation

[Tasneem Kausar]

You can directly extend time with gmx covert-tpr -s old.tpr -o new.tpr
-extend 20000

On 18 May 2017 15:34, "Kashif" <kashifzamir180.mk at gmail.com> wrote:

> It means I should conver my md.mdp file for 40 ns from 20 ns in the same
> folder and then run this command ...
>
> grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -extend
>
> after that this command...
>
> mdrun -deffnm md_0_1
>
> Please suggest the correct command if it is not correct.
>
> regards
>
> kashif
>
>
> On Wed, May 17, 2017 at 3:22 PM, Kashif <kashifzamir180.mk at gmail.com>
> wrote:
>
> > I have already run my 20 ns md simulation of my protein. The log file is
> > showing completion of my 20 ns data. I have also done analysis by using
> > trjconv command and g_rms.
> > Now I want to increase my simulation at least for 20 ns more and make my
> > data of protein simulation for 40 ns. Kindly help for continuation of my
> > simulation. I have used this command but it did not help and shows error.
> > command:   mdrun -deffnm md_0_1 -cpi md_0_1.cpt -append
> >
> > error:
> > NOTE: 23 % of the run time was spent communicating energies,
> >       you might want to use the -gcom option of mdrun
> >
> >                      Core t (s)    Wall t (s)        (%)
> >        Time:       25.000        2.843         879.2
> >                       (ns/day)        (hour/ns)
> > Performance:        0.061      394.912
> > Finished mdrun on node 0 Sat Apr 29 11:46:36 2017
> >
> > regards
> > kashif
> >
> --
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