Re: SMD under NPT ensemble

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Mon Mar 19 2012 - 14:35:22 CDT

Hi Yi,

Basically the Langevin thermostat does not conserve momentum (which is
why you sometimes need to set com motion to zero), and hence it is
Galilean invariant. This is not much of a problem in a system where
the net velocity of the system is zero, but in the case of constant
velocity SMD it is a problem. The Lowe-Andersen thermostat, however,
does conserve momentum and so avoids this issue.

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
------------------------------------------------------------------------------------------------------

On Mon, Mar 19, 2012 at 2:09 PM, Wang Yi <dexterwy_at_gmail.com> wrote:
> Hi Johan,
>
> Would you mind elaborating a bit more on the topic of Galilean invariance?
> In Dr. Schulten's original paper on NPT ensembles of SMD, I didn't see the
> Galilean invariance explicitly mentioned.
>
> Thanks~
> ___________________________
>
> Yi (Yves) Wang
> Duke University
>
>
>
>
>
> On 2012-3-19, at 下午12:28, johan strumpfer wrote:
>
> 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
> ------------------------------------------------------------------------------------------------------
>
>
>
> 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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