[gmx-users] Energy Conservation with 4fs timestep
ilchorny at gmail.com
Wed Apr 1 20:20:59 CEST 2009
rlist 1.3 did the trick, thanks. Why did I not see this problem with
2009/4/1 Berk Hess <gmx3 at hotmail.com>
> > 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
> > > 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
> neighborlist update frequency (somewhere around 10 steps).
> We should automate the choice of rlist such that the user does not need to
> about this.
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