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

[Berk Hess]

Yes, but that is done before starting the simulation, so your total energy
will still be nicely constant.

Berk

> Date: Mon, 14 Jun 2010 11:55:18 +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
> 
> 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
> -- 
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