[gmx-users] The equilibrium before REMD simulations

[Justin A. Lemkul]

ÏéÇ« ¿× wrote:
> Dear GMX users, I am puzzled about some technical details regarding to the
> REMD simulation and eager for your generous help. With the purpose to explore
> the additional conformational space of the protein, I want to employ the REMD
> method in Gromacs. However, I noticed that in almost all of the papers about
> REMD, a short equilibrium with NPT or NVT was performed for each replica
> respectively before the final REMD run. But i think the initial structure of
> each replica for REMD run is thus different due to the respective equilibrium
> and may somewhat go against the concept of replicas which i suppose should
> have same initial structures while with different temperatures. So my
> question is whether we should or not perform the NVT or NPT equilibrium
> before REMD simulations BTW and why? BTW, i also want to know which ensemble

Yes, always equilibrate.  Otherwise, your systems will almost certainly not be 
stable.  Position restraints are typically applied to the solute of interest 
during the initial equilibration, making initial differences almost insignificant.

> should we use in REMD because some papers use NPT while others use NVT. 

Pressure coupling algorithms frequently break down at high temperature, so NVT 
is often used.

-Justin

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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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