From: felmerino_at_uchile.cl
Date: Mon Mar 19 2012 - 16:11:54 CDT
I think we had a similar discussion a couple of days ago in the list. If you are going to use an NPT ensemble (i will assume here that using the nose-hover-langevin barostat) then it does not matter if you use langevin or andersen for the temperature, the dynamics of the system will be modified from the white noise introduced by the pressure control and you will kill the momentum conservation. Of course that won't happen in the NVT ensemble. I suppose that the final choice depends in the end of what you are trying to obtain from the MD.
Regards
Felipe
----Mensaje original---- De: dexterwy_at_gmail.com Fecha: 19-mar-2012 14:09 Para: <johanstr_at_ks.uiuc.edu> CC: "raghav singh"<raghavbioinfo_at_gmail.com>, <namd-l_at_ks.uiuc.edu> Asunto: Re: namd-l: SMD under NPT ensemble 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 ??12:28, johan strumpfer wrote:
Raghav,Namd can do this, but you should be careful of which thermostat youuse. The Langevin thermostat is not Galilean invariant, so you shouldnot use it when doing SMD. To get around this you should use theLowe-Andersen thermostat which is Galilean invariant. In practice I'vealso found that NVT to give more reliable results than NPT.Cheers,Johan------------------------------------------------------------------------------------------------------Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstrPh.D. CandidateTheoretical and Computational Biophysics Group3115 Beckman InstituteUniversity of Illinois at Urbana-Champaign405 N. MathewsUrbana, 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 ??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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