[gmx-users] The equilibrium before REMD simulations
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.
--- 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« ¿×
> > 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
> That is a standard REMD workflow. Do check out some
> literature for REMD simulations similar to your system.
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