On 12/1/13 2:48 AM, kiana moghaddam wrote:
Dear
GMX Users
I
want to run NVT equilibration and NPT equilibration (after
NVT) for DNA-ligand interaction and want to increase temperature
gradually i.e.
from
0 to 300 K over a 100 ps, but i have some questions about this process:
when
I use simulated anealing in NVT as following
annealing_time
= 0 15 30 45 60 80 100
annealing_temp = 0
50 100 150 200 250 300
I
don't know how to change gen_vel.
> gen_vel = yes
gen-seed = 173529
is
correct? or the gen_vel =No is correct?
(After NVT equilibration, I want to equilibrate system during NPT condition at
300 K.)
Set "gen_vel = yes" at the beginning of the annealing run, then "gen_vel = no"
for all subsequent steps, in which you preserve the previous ensemble using
checkpoint files.
-Justin
--
==================================================
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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