[gmx-users] gen_vel

[Justin Lemkul]

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

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

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