[gmx-users] simulation at different temperature

Justin Lemkul jalemkul at vt.edu
Wed Jul 5 23:45:21 CEST 2017

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 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


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