[gmx-users] problem in extending MD in Gromacs 2018

[Alex]

Hi Ladan,
Just suppose your 10000 steps MD simulation has already finished and you
intend to extend your simulation for further 5000 steps, so;
    gmx convert-tpr -s 10000.tpr -nsteps 15000 -o 15000.tpr
gives you a new .tpr file by which you can continue your simulation as
below:
    gmx mdrun -s 15000.tpr -cpi 10000.cpt -append
The results would be appended to your initial files accordingly.
Cheers,
Alex

On Mon, Oct 15, 2018 at 5:48 PM Ladan Mafakhe <stud.l_mafakher at pasteur.ac.ir>
wrote:

> Hi
>
> I use Gromacs 2018. I ran one of my MD run. after finishing my MD I want
> to extend my PDB. I used these command as you say in Gromacs
> documentation2018. but my MD run did not extend and it started from the
> first step. why this happened and how I can fix it. the commands that I
> used:
>
> gmx convert-tpr -s md_0_1.tpr -o md-ex.tpr -until 40000
>
> gmx mdrun -v -s md-ex.tpr -e md-ex.edr -c md-ex.gro -o md-ex.trr -g
> md-ex.log
>
> and I used this extending command too but I got same error:
>
> gmx convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr
>
> gmx mdrun -s next.tpr -cpi state.cpt
>
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