[gmx-users] Dividing an MD run

[Guillem Prats Ejarque]

Thanks a lot for your help. 

But in my case, the tpr file that I have ran in the first step is not useful, because is set to 8 ns, and I want to perform a total run of 20 ns. So, to do the next part of the ran, I have to prepare a new tpr of 12 ns and run since the last checkpoint? Would be this ok?

grompp -f md_8ns.mdp -c equilib.gro -t equilib.cpt -p topol.top -n index.ndx -o md_8ns.tpr

mdrun -nt 16 -v -deffnm md_8ns

grompp -f re_md_12ns.mdp -c md_8ns.gro -t md_8ns.cpt -p topol.top -n index.ndx -o re_md_12ns.tpr

mdrun -nt 16 -v -deffnm -cpi md_8ns.cpt md_8ns 

Regards,

Guillem

On 3/3/16 6:13 PM, Guillem Prats Ejarque wrote:
> So, If I have an mdrun running now, but I didn't set in this run an -cpo flag, I cannot continue from the last point of this run?
>

Checkpoint files are written at the interval specified by -cpt.  Unless you've
set that to 0 (or -1, I can't remember) then mdrun will write them
automatically.  You should see that happen within a few minutes (whatever the
value of -cpt is set to, 15 by default).

-Justin

>
> On 3/3/16 5:23 PM, Guillem Prats Ejarque wrote:
>> Hi,
>>
>>
>> I have to do a production MD in an HPC cluster and due to the company's policy I have to resubmit the job in the queue everyday. This is probably a stupid question, but, to resubmit it starting from the point where I left it, do I only have to run the MD again with the output files of the previous one, like this?
>>
>>
>> grompp -f remd.mdp -c md.gro -t md.cpt -p topol.top -n index.ndx -o remd.tpr
>>
>> mdrun ....
>>
>>
>> or should I take into account anything else? Will I obtain the same results if I do the dynamic in a single run, or in several steps?
>>
>>
>
> Once you've created the .tpr file, all you need to do is add -cpi -append to
> your mdrun command to load from the last checkpoint.  Nothing more to it.  You
> can also use -maxh to ensure a clean exit when you hit the wallclock limit.  The
> continuation from the checkpoint is exact.
>
> -Justin
>
> --
> ==================================================
>
> 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
>
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--
==================================================

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

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