[gmx-users] The equilibrium before REMD simulations

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 15 02:10:12 CET 2011

On 15/11/2011 11:55 AM, ÏéÇ« ¿× wrote:
> 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.

Yes, NPT REMD appears to be quite sound. However, unless you actually 
want to make measurements of physical observables at the higher 
temperatures, there's no requirement that the higher ensembles 
correspond to any particular physical model - see things like resolution 
replica-exchange. A coordinate mapping, a sufficiency of PE overlap and 
the possibility of barrier crossing are all that is required for useful 
replica exchange.

There are also some technical issues associated with density in NPT. 
Because the lists of non-bonded interactions are shorter when the 
density is lower, the higher-temperature replicas have less work to do, 
so have to waste some computer time waiting for the lower ones to 
finish. That's not a big deal, but if you want to use PME and maintain 
accuracy, the Fourier grid density should change inversely with particle 
density, and that gets a bit messy.

Issues with the size of the integration time step at high P and T have 
also been known to occur.


> 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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