On 12/1/13 2:48 AM, kiana moghaddam wrote:
GMX Users

want to run NVT equilibration and NPT equilibration (after
NVT) for DNA-ligand interaction and want to increase temperature
gradually i.e.
0 to 300 K over a 100 ps, but i have some questions about this process:
I use simulated anealing in NVT as following
=  0  15  30  45   60  80  100
annealing_temp          = 0
  50 100 150 200 250 300
don't know how to change gen_vel.

  > gen_vel                                 = yes

gen-seed                 = 173529
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 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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