[gmx-users] No Energy Conservation in NVE simulation of liquid mixtures

[Tsjerk Wassenaar]

Hey :)

Errm, you subtract the overall linear momentum. That affects the
kinetic energy, decreasing it, doesn't it?

Tsjerk

On Mon, Jun 14, 2010 at 10:59 AM, Berk Hess <gmx3 at hotmail.com> wrote:
> Hi,
>
> Why not?
>
> Berk
>
>> Date: Mon, 14 Jun 2010 08:19:30 +0200
>> Subject: Re: [gmx-users] No Energy Conservation in NVE simulation of
>> liquid mixtures
>> From: tsjerkw at gmail.com
>> To: gmx-users at gromacs.org
>>
>> Hi Godwin,
>>
>> I noticed you're removing center of mass motion, which you shouldn't for
>> NVE.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Mon, Jun 14, 2010 at 4:09 AM, Godwin Kanu <biggugo at live.com> wrote:
>> >
>> > Hi GMX Users,
>> >
>> > I am having difficulties getting gromacs to conserve energy (I
>> > experience a
>> > directional drift) when I do an NVE simulation of mixtures (i tried both
>> > THF/water and water/methanol). But when I do simulation of a pure liquid
>> > it
>> > works great. I have tried tinkering with a lot of stuff including the
>> > electrostatic interaction and making sure the combination rules for
>> > non-bonded interactions work as it is supposed to. I usually start with
>> > an
>> > NVT simulation to equilibriate it at the temperature I'm interested in
>> > before removing the temperature bath to do an equilibration run in
>> > the microcanonical ensemble. I have attached some of my input files for
>> > you
>> > to examine. I'm using GROMACS version 4.0.5 parallel.
>> > Thanks
>> >
>> > Godwin.
>> >
>> >
>> >
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>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> Groningen Institute for Biomolecular Research and Biotechnology
>> University of Groningen
>> The Netherlands
>> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands