[gmx-users] time in restarting job

[Justin Lemkul]

On 7/1/16 8:12 AM, Marta Wisniewska wrote:
> Dear Users,
>
> I am a bit confused. I'd like extend my simulation. For it I used command:
> grompp -f prod.mdp -c prod.tpr -o prod_ext.tpr -t prod.cpt
> mdrun -s prod_ext.tpr
>
> But now I have 2 simulation (first md) 0-100ns and extended 0-50ns. How to
> extend time? Because after trjcat .trr files I'd like to have 150ns
> simulations, not 100ns and 50ns, what I have now.
>

If you use grompp to extend runs, you need to change tinit and init_step, 
otherwise the run starts from t=0.  This can be corrected with trjcat -settime 
when concatenating, otherwise use the simpler approach without grompp:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4_and_Newer

-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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