[gmx-users] simulated anealing

[kiana moghaddam]

ِDear Jastin 

Thanks your reply. In the first step (NVT equilibration) for heating system by simulated anealing from 0 to 300 K, what is the value of gen-temp?

Thanks for your time and consideration.
Best Regards
Kiana




On Sunday, December 1, 2013 4:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 



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

-- 
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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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