Re: membrane simulation at high Temp

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 04 2011 - 19:08:22 CDT

On Fri, Nov 4, 2011 at 7:58 PM, Chris Harrison <charris5_at_gmail.com> wrote:

> Temperature based REMD requires an NVT ensemble, which imposes a constant
> volume. Just make sure you're running in an NVT ensemble as per your NAMD
> configuration, ie, constant temp and volume.
>

in theory, NPT should be possible, too, but that requires to include
a term considering the p*V work into the metropolis criterion.
in practice that typically translates to "use NVT", though.

cheers,
    axel.

>
> Best,
> Chris
>
> On Friday, November 4, 2011, Jiao, Dian NMN (-EXP) <dnjiao_at_sandia.gov>
> wrote:
> > The equilibrated system at 600k would probably have a much larger volume
> than 300k. Ultimately, I will run REMD at different temperatures. In order
> to make the replica exchange, the two neighboring simulations should have
> the same volume. Is that right? Or in REMD, I should fix the size of the
> water box regardless of the system temperature?
> > From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> > Date: Fri, 4 Nov 2011 17:56:12 -0400
> > To: Dian Jiao <dnjiao_at_sandia.gov>
> > Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> > Subject: Re: namd-l: membrane simulation at high Temp
> >
> > Perhaps constant volume?
> >
> > On Fri, Nov 4, 2011 at 5:50 PM, Jiao, Dian NMN (-EXP) <dnjiao_at_sandia.gov>
> wrote:
> >>
> >> Hi all,
> >> I was trying to run simulations for an ion channel embedded in a lipid
> bilayer. With constant area restraint, I was able to run 10-ns MD
> simulation for the system at 300k without any problem. However at high
> temperature (600k), the waters and lipids start to expand in both
> directions of Z-axis. If I turn on the surfacetension, they would expand in
> X and Y directions instead. Since NAMD does not allow to have both constant
> area and surface tension at the same time, I wonder if there is a way to
> exert forces in X, Y and Z directions to hold the system together.
> >> Thanks.
> >> Dian
> >
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 773-570-6078
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:31 CST