[gmx-users] simulation at different temperature

[Alex]

Sure, and I suggested that alternative.

Alex

On Wed, Jul 5, 2017 at 3:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/5/17 3:09 PM, Alex wrote:
>
>> I don't understand the objection. This _is_ full dynamics of the system
>> containing behavior at all desired temperatures.
>> After it's done, you can easily split trajectories into the desired
>> annealing regions. Alternatively, you could simply script this as a
>> sequence of separate runs based on mdp's with gradually increasing T,
>> simply throw away a few first ns of each simulation before analyzing.
>>
>>
> I don't see the benefit of annealing.  A big challenge (with any
> simulation) is sampling, and a single run of increasing temperature leaves
> you waiting for a long time (because you need sufficient time at each
> temperature) and you still only have one run.  If all one cares about is
> temperature dependence of dynamics, I'd just simulate N replicates at each
> temperature, independently, and acquire data in a much more efficient
> manner.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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