Native protein is very compact i,e its volume is minimum. However, a
unfolded protein is more open. Therefore, the volume of a completely
unfolded protein is maximum.
On Thu, Mar 14, 2013 at 7:47 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> 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 Fri Mar 15 2013 - 09:30:04 PDT
