Equilibrate NPT at the desired temperature before switching to NVT.
Bill
sudipta <sudipta.mml.gmail.com> wrote:
> 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 - 16:30:04 PDT
