[gmx-users] Brownian dynamics

[Yin Jian]

Hi Berk,
I am looking for a way to be able to run MD faster without
Explicit solvent component. Brownian dynamics (I mean langevin
Dynamics) is way out I think. But I am not sure the package
Implemented in Gromacs is a good one or not yet. Since I have
Seen no one using it in the literature yet, right?

Happy new year and merry Xmas


Regards,
Yin Jian

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Berk Hess
Sent: Thursday, December 20, 2007 10:21 PM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] position restraints with npt ensemble

It will be problematic, so I think it would be better to do NVT
simulations.
Gromacs 4.0 will support scaling of position restraints coodinates
in two different ways: all coordinates or only the center of mass.
If you really need it you can try to use the current CVS version,
but there all still things being changed and there might be bugs.

Berk.


>From: "Zhou Bo" <zhoubo81 at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: <gmx-users at gromacs.org>
>Subject: [gmx-users] position restraints with npt ensemble
>Date: Thu, 20 Dec 2007 21:21:49 +0800
>
>Hi gmx-users,
>
>I want to restrain some atoms of a certain protein in water for
production,
>but I am not sure whether it makes sense to make NPT simulations with
>position restraints. I mean if the coordinates of the restrained atoms
are
>not scaled, it would be problematic in pressure coupling. Thanks in 
>advance.
>
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