[gmx-users] overcome the integration problem (installing CVS)

Berk Hess gmx3 at hotmail.com
Wed Apr 11 17:30:50 CEST 2007

>From: "Michael Shirts" <mrshirts at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] overcome the integration problem (installing CVS)
>Date: Wed, 11 Apr 2007 11:15:08 -0400
>Hi, all-
>>I would like to add that for a constant temperature ensemble the effect
>>of this fix is neglegible.
>>It is only useful for constant NVE simulations.
>I think this might need some qualifications. If the constant
>temperature dynamics are based inherently on NVE dynamics, they must
>be affected similarly.  For example, for Nose-Hoover thermostats,
>there exists a conserved quantity.  I would expect that this fix would
>also improve that conserved quantity, wouldn't it?

It would.
Although I would still argue that when using a thermostat there
is in most cases no "useful" quantity that would be affected
by the current, very small, velocity inaccuracies.

>One feature that would be useful is that for any algorithm that has a
>"conserved energy-like" quantity, there should be an entry in the .edr
>file with that quantity.  It would be a useful check for algorithmic
>consistency.  I don't think this is yet in GROMACS, though I could be
>wrong -- I haven't examined the CVS that recently.

It is not (yet) in Gromacs, but it would indeed be useful to have it.


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