[gmx-users] How to extend simulation?

[ZHANG Cheng]

Thank you. So if the below is correct, and it will run for 100 ns?


convert-tpr -s previous.tpr -extend 100000 -o next.tpr
gmx mdrun -deffnm next -cpi previous.cpt





------------------ Original ------------------
From:  "Justin Lemkul";<jalemkul at vt.edu>;
Date:  Tue, Apr 4, 2017 02:12 AM
To:  "gmx-users"<gmx-users at gromacs.org>; 

Subject:  Re: [gmx-users] How to extend simulation?





On 4/3/17 2:07 PM, ZHANG Cheng wrote:
> (Following Justin's suggestion)
>
>
> Dear Gromacs Researchers,
> My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to extend it to 100 ns.
>
>
> As shown on
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
>
> Should I use the following two lines of code for the files in the same folder?
> If the "deffnm" is set correctly?
> But in this case, will the new simulation still only have 10 ns?
>

No.

>
> convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr

If you replace "timetoextendby" with some sensible value of time (ps), then this 
means "next.tpr" will specify some longer amount of time to run.

> gmx mdrun -deffnm next -cpi previous.cpt

...which is then passed to mdrun here.  This says "run the longer simulation 
specified in next.tpr, but start from the point specified in previous.cpt rather 
than starting over from time zero."

-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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