[gmx-users] The equilibrium before REMD simulations

ÏéÇ« ¿× iconsdkxq at yahoo.com.cn
Tue Nov 15 01:55:49 CET 2011

Thanks for everyone's prompt reply! However, i still puzzled why we should use NVT rather than NPT in REMD simulation. As we know that isothermal-isobaric ensemble may be more relevant to the realistic experimental conditions. If the highest temperature was no more than 400K ( i think it is not very high) and the pressure coupling may still work, should NPT be a better choice? Or the NPT method would impair the physical meanings of REMD, however, some NPT examples were depicted in some papers and also in our mailing list.

Best regards!
Xiangqian Kong

--- On Mon, 11/14/11, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] The equilibrium before REMD simulations
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Monday, November 14, 2011, 11:53 PM
> On 15/11/2011 2:50 AM, ÏéÇ« ¿×
> wrote:
> > Dear Justin,
> >    Thanks for your prompt reply!
> >    As you say, we should equilibrium each
> replica at its initial target temperature. So i guess we may
> do the followings: First, after the minimization and
> heating, we use NPT to equilibrium the density of the
> system. And then with the same initial system,equilibrium
> every replica at their target temperature with NVT ensemble
> to avoid the instability during REMD and keep the volume
> constant among the replicas. Finally, do the REMD
> simulations. Is this workflow reasonable enough and do you
> have any better guide? Any suggestions will be greatly
> appreciated!
> > 
> That is a standard REMD workflow. Do check out some
> literature for REMD simulations similar to your system.
> Mark
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