Re: [AMBER] NVT and NPT ensemble

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Wed, 23 Jul 2014 09:50:00 +0530

 

Thank you sir

I have got one of the same answer as in this discussion that during MD
simulation of biological macromolecule chances of change in shape thus
NPT should be used for MD simulations macromolecule (when shape changes
is expected) because volume will be change. If there is no significant
change in shape of macromolecule NVT can be use.

On 2014-07-23 8:24 am, Raman Parkesh wrote:

> You can see more discussion here
> http://comments.gmane.org/gmane.science.biology.gromacs.user/52915 [1]
>
> On 21 July 2014 14:25, Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
> wrote:
> Please follow this thread to get some insight http://archive.ambermd.org/201103/0431.html [2] On Mon, Jul 21, 2014 at 10:17 AM, Sangita Kachhap <sangita.imtech.res.in> wrote: NVT and NPT are two commonly used ensemble during MD simulation of biomolecules. NPT must be used during equilibration just before changing to constant volume ensemble. So during production run NVT or NPT which one should be prefer and why -- Sangita Kachhap SRF C/O Dr. Balvinder Singh BIC IMTECH _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber [3] -- Thanks & Regards; Soumendranath Bhakat _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber [3]

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-- 
Sangita Kachhap
SRF
C/O Dr. Balvinder Singh
BIC
IMTECH
 
Links:
------
[1] http://comments.gmane.org/gmane.science.biology.gromacs.user/52915
[2] http://archive.ambermd.org/201103/0431.html
[3] http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jul 22 2014 - 21:30:02 PDT
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