[gmx-users] Re: Energy Drift in Gromacs 4.0
gmx3 at hotmail.com
Thu Mar 12 12:42:13 CET 2009
Everything depends completely on how much drift you are talking about.
There will always be energy drift, it is just a question how much.
In general shifted potentials will be cheaper (and lead to less energy drift)
than setting nstlist to 1, but for most purposes a bit of energy drift is no problem.
> Date: Thu, 12 Mar 2009 10:55:47 +0100
> From: degaetani at dcci.unipi.it
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: Energy Drift in Gromacs 4.0
> Even if a system is not well equilibrated (but not so far from
> equilibrium) ,energy should be conserved in NVE ensemble.
> Try to lower the nstlist from 10 to 1 i.e. renew every time the
> neighbourlist. In systems I have studied, that is the key that improve
> much more energy conservation. It works even without switching of VdW
> Luca Dre Gaetani
> > Message: 1
> > Date: Thu, 12 Mar 2009 13:59:11 +1100
> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
> > Subject: Re: [gmx-users] Re: Energy Drift in Gromacs 4.0
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <49B87A7F.30807 at anu.edu.au>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> > Ilya Chorny wrote:
> >> If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE
> >> simulation they should counter balance. I am leaking K.E. somewhere. I
> >> reran with a relaxed P.E(t) and saw the same behavior. This is
> >> happening both at 2 and 4 fs so its not a time step issue. Any thoughts?
> >> I thought it might be COM removal so I turned it off to no avail.
> > "going down" is seriously unhelpful. I told you you needed to
> > equilibrate before measuring such things. If you want people to take
> > your problem seriously, you'll need to announce that you have
> > equilibrated and for how long and in what ensembles, etc. If you're
> > having a problem, you need to demonstrate what areas you feel are not
> > causing it. We're not your family doctor who will ask a pile of
> > questions to find out the problem :-)
> > Mark
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users