On 11/26/13 11:48 PM, Mahboobeh Eslami wrote:
Hi Dear Gmx Users,
Do not just following procedure can be usedby gen_vel:
NVT gen_vel = yes
gen_temp=300
gen_seed=-1
NPT gen_vel=no
MD gen_vel=no
i want to study the changing of velocity in md stage. Can I use the following
method:
NVT gen_vel = yes
gen_temp=298
gen_seed=-1
NPT gen_vel=no
MD gen_vel = yes
gen_temp=298
gen_seed=-1
I don't understand what purpose this serves. If you re-generate velocities
after equilibration, what was the purpose of equilibration in the first place?
You trash the previous ensemble, and depending on the algorithms you're using
for temperature and pressure coupling, you run the risk of simply crashing the
simulation. If you're looking for better sampling through independent
trajectories (from different initial velocities) the first approach does that
just fine.
-Justin
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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