[gmx-users] Large fluctuation of protein temperature with nose hoover thermostat

[ABEL Stephane 175950]

OK thank you Omer, for you response



The group PROTEIN isn't very large as the group NONPROTEIN, therefore its
total kinetic energy fluctuates more.
--Omer.

On Wed, Sep 16, 2009 at 12:10, Stephane Abel <Stephane.Abel at cea.fr> wrote:

> tc-grps = Protein Non-Protein ; two coupling groups - more accurate
> tau_t = 0.4 0.4 ; time constant, in ps
> ref_t = 310 310 ; reference temperature, one for each group, in K

Energy Average RMSD Fluct. Drift Tot-Drift
>
> -------------------------------------------------------------------------------
> Temperature 310 2.46886 2.46886 6.12135e-07 0.0171398
> T-Protein 310 32.1134 32.1117 -4.10352e-05 -1.14898
> T-Non-Protein 310 2.47549 2.47548 8.55869e-07 0.0239643
>
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Message: 4
Date: Thu, 17 Sep 2009 01:39:15 -0700
From: Darrell Koskinen <darrellk at ece.ubc.ca>
Subject: [gmx-users] Periodic Boundary Conditions & Location of Atoms
	Near	Box Edges
To: gmx-users at gromacs.org
Message-ID: <4AB1F5B3.5060106 at ece.ubc.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Dear GROMACS Gurus,
In order to correctly model an infinite graphene sheet using periodic 
boundary conditions, should the box edges be located at the midpoints 
between the atomic bonds?

Thanks.

Darrell


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