[gmx-users] parameters in *.mdp files

Justin Lemkul jalemkul at vt.edu
Sun Aug 19 16:09:27 CEST 2012

On 8/19/12 9:29 AM, Shima Arasteh wrote:
> Thanks for your reply.
> Yes, using a better thermostat doesn't mean I have a longer simulation. But, a better thermostat has more ab-initio terms, which I think the calculation of them might be time consuming. That's why I guess I will have a longer simulation ( the time which the computer spends to simulate a system for adjusted time such as 50 ns).

I have never seen an appreciable difference between the performance obtained 
with different thermostats.  The time taken for coupling algorithms is 
negligible compared to the vastly more expensive calculations done during an MD 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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