[gmx-users] Extending simulations

[masoud keramati]

sorry with my question

is it true that for extending simulation use the following code?

gmx grompp -f md.mdp -c md.gro -t md.trr -p topol.top -o md2.tpr
gmx mdrun -deffnm md2

*md.gro and md.trr is files for first run

On 12/22/15, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 12/21/15 7:00 PM, Soumya Lipsa Rath wrote:
>> Dear Mark and Chandan,
>>
>> Thank you so much for the information. I was indeed using a wrong tpr
>> file.
>> I will include the -cpi state.cpt flag during the tpbconv step.
>>
>
> You don't need -cpi with tpbconv, only in mdrun.
>
> -Justin
>
>> Thanks,
>>
>> Soumya
>>
>> On Mon, Dec 21, 2015 at 12:30 PM, Soumya Lipsa Rath
>> <soumyalipsabt at gmail.com
>>> wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I am trying to extend my simulation for 200ns by using:
>>>
>>> tpbconv_mpi -s topol.tpr -extend 200000 -o topol2.tpr
>>> mdrun_mpi -s topol2.tpr -cpi state.cpt -append -maxwarn 5 >&
>>> grompp_output.log
>>>
>>> However, my simulation has only extended for 50ns. Am I doing something
>>> wrong?
>>>
>>> Thanks,
>>>
>>> Soumya
>>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-request at gromacs.org.
>