[gmx-users] Energy Conservation with 4fs timestep

Berk Hess gmx3 at hotmail.com
Wed Apr 1 09:26:51 CEST 2009

> Date: Wed, 1 Apr 2009 14:15:05 +1100
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Energy Conservation with 4fs timestep
> Joe Joe wrote:
> > Hi,
> > 
> > I get good conservation when running NVE in gromacs with 4 fs when I use 
> > PME-switch for electrostatics but not so good when I use switch. Any 
> > thoughts why that would be? Params shown below.
> Finite cutoffs (such as used with "switch") are intrinsically unlikely 
> to conserve energy.
> Mark

That is not right.
Finite cut-off's such as switch and shift are purposely designed to conserve energy.
Switch is not particularly good though, since the switching introduces large forces.
I would advise to use PME-switch or reaction-field-zero for electrostatics and shift for vdw.

But the main problem in your setup seems to be the 0.1 nm buffer between the cut-off
and rlist. In general you will need a buffer of 0.25 to 0.3 nm.
You can use rlist=-1 to get exact integration and then vary rlist to get a reasonable
neighborlist update frequency (somewhere around 10 steps).
We should automate the choice of rlist such that the user does not need to worry
about this.


Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090401/287dabc4/attachment.html>

More information about the gromacs.org_gmx-users mailing list