[gmx-users] REMD equilibration

[Erik Marklund]

23 mar 2012 kl. 11.37 skrev Justin A. Lemkul:

> 
> 
> francesco oteri wrote:
>> I understand,
>> I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it?
> 
> Another very real concern is the stability of the simulations under NPT.  At higher temperatures, the box itself may vary more widely and when the system is exchanged, the algorithms can fail.  This phenomenon has been reported by a number of other users.  With NVT, this does not happen.
> 
> -Justin

Very true. The benefit from NPT is on the other hand that the replicas can be more distant in temperature space, so if it works then NPT is more efficient.

Erik

> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
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erikm at xray.bmc.uu.se
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