[gmx-users] velocity generation

kiana moghaddam ki_moghaddam at yahoo.com
Thu Dec 5 19:22:17 CET 2013

Dear Jastin

Thanks your reply. as your email, I will generate velocity in NVT step with simulated annealing from 0 to 300K. What should be gen_temp value? Is 300 K correct?

Best Regards

On Thursday, December 5, 2013 9:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 12/5/13 12:36 PM, kiana moghaddam wrote:
> Dear GMX user
> I want to use NVT to heat my system (DNA-ligand) from 0 to 300K then NPT at 300 K in equilibration step.
> I 'm very confused about velocity generation.
> I use gen_vel= no in the first step (NVT) then generate velocity in the NPT step at 300 K. After that, in production step I use gen_vel= no. Is my process correct?

If you generate new velocities at the outset of NPT, it introduces new 
instability and basically negates any benefit of having done any prior 
equilibration.  Preserve the velocities from NVT (via the .cpt file) when 
continuing to NPT.  Rule of thumb: do not generate velocities for any step in 
the protocol that is not the very first one.  There are exceptions, but they are 
generally rare.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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