From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Mon Mar 19 2012 - 11:28:25 CDT
Raghav,
Namd can do this, but you should be careful of which thermostat you
use. The Langevin thermostat is not Galilean invariant, so you should
not use it when doing SMD. To get around this you should use the
Lowe-Andersen thermostat which is Galilean invariant. In practice I've
also found that NVT to give more reliable results than NPT.
Cheers,
Johan
------------------------------------------------------------------------------------------------------
Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstr
Ph.D. Candidate
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
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On Mon, Mar 19, 2012 at 11:20 AM, Wang Yi <dexterwy_at_gmail.com> wrote:
> There are instructions on how to do SMD in NAMD, using either the
> configuration file or the latest ColVar technique.
>
> You can find them in the NAMD manual online.
> ___________________________
>
> Yi (Yves) Wang
> Duke University
>
>
>
>
>
> On 2012-3-19, at 上午11:12, raghav singh wrote:
>
> Hello All,
>
> I wanted to know about SMD simulation using NPT ensemble...
> NAMD has this freedom or not... any suggested article would be off great
> help.
>
> Thank You all
>
> regrads
> Raghav
>
>
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