How would structural changes increase volume?
sudipta <sudipta.mml.gmail.com> wrote:
> Is that enough? If some structural changes occur during REMD.
>
> On Thu, Mar 14, 2013 at 7:12 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > 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 - 17:00:05 PDT
