[gmx-users] velocity generation
ki_moghaddam at yahoo.com
Thu Dec 5 19:22:17 CET 2013
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?
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
Justin A. Lemkul, Ph.D.
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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