[gmx-users] md continuation

Kashif kashifzamir180.mk at gmail.com
Thu May 18 12:04:22 CEST 2017

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.



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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