there is no reason at all for the replicas to have the same initial
structures.
Amber uses NVT- if you want NPT, you have to account for this explicitly,
see work by Garcia and others.
On Mon, Nov 14, 2011 at 9:15 AM, ÏéÇ« ¿× <iconsdkxq.yahoo.com.cn> wrote:
> Dear AMBER 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 should we use in REMD because some
> papers use NPT while others use NVT.
> Thanks in advance!
> Best regards!
> Xiangqian Kong
>
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>
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Received on Mon Nov 14 2011 - 06:30:04 PST
