Hi Niel,
Thank you very much for your reply. Yeah, I noticed that most of the people
had used NVT instead of NPT. Nobody has not put any straightforward reason
for choosing NVT over NPT. However, is the simulation of protein system at
high temperature in NVT ensemble reasonable? When we increase the
temperature of such system then the protein molecule will be expanded and
it looks for some space. However, NVT ensemble doesn't compromise any
space. I am curious about this.
Another issue is use of explicit solvent. Most of REMD study has been
performed in implicit solvent environment. Is there any inherent reason
behind this except computational cost.
Best
Sudipta
On Thu, Mar 14, 2013 at 6:51 PM, Niel Henriksen <niel.henriksen.utah.edu>wrote:
> Sudipta,
>
> AMBER does not support (as far as I know) temperature REMD simulations
> in the NPT ensemble. Only NVT is supported. There has been some
> discussion
> in the literature of the impact of NVT on REMD although I do not have the
> citations on hand. Most papers use NVT with explicit solvent REMD.
>
> Good luck,
> --Niel
>
> ________________________________________
> From: sudipta [sudipta.mml.gmail.com]
> Sent: Thursday, March 14, 2013 11:06 AM
> To: amber.ambermd.org
> Subject: [AMBER] REMD simulation
>
> Hi All,
>
> Is the REMD simulation useful for explicit solvent system. If so, then what
> will be ensemble. I think simulation at high temperature in explicit
> solvent require to allow volume fluctuation and therefore the reasonable
> ensemble should be NPT. However, using AMBER REMD, most of the implicit
> solvent system has been performed in NVT condition. But I want to apply it
> in explicit solvent system. Any suggestion!
>
> Best
> Sudipta
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Received on Thu Mar 14 2013 - 16:30:03 PDT
