[gmx-users] Center of mass motion removal

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jun 3 08:44:35 CEST 2015


Hi Tuong Vy,

There is no difference in practice except for raising the error. The
developers can't try catching all possible foolish things people could try
with an error. Also, if you think of fooling the program in this way, you
may be assumed to know what you're doing (and why you wouldn't need to
worry about flying ice cubes).

Cheers,

Tsjerk
On Jun 3, 2015 8:23 AM, "Vy Phan" <phanvy120690 at gmail.com> wrote:

> Dear Tsjerk and all,
> If I set up the comm-mode =None ( COM motion is not removed), i got the
> Warning : numerical rounding errors can lead to build up of  kinetic energy
> of the COM and the simulation can not run.
> I think comm-mode =None and {comm-mode =Linear , nstcomm  > nststeps) is
> similar meaning.
> I misunderstand something?
> Could you explain more?
>
> Many Thanks
> Tuong Vy
>
> 2015-06-03 15:11 GMT+09:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:
>
> > Hi Tuong Vy,
> >
> > Right. If COMM is removed every N steps and the simulation runs for M < N
> > steps, then COMM will never actually be removed.
> >
> > Cheers,
> >
> > Tsjerk
> > On Jun 3, 2015 4:44 AM, "Vy Phan" <phanvy120690 at gmail.com> wrote:
> >
> > > Dear all,
> > > I wonder when I set the comm-mode =Linear , and nstcomm
> > > (frequency for COM motion removal)  > nststeps (maxinum number of
> steps),
> > > the MD simulation can be performed.
> > >
> > > I think the nstcomm > nsteps mean COM motion is not removed (the MD
> > > simulation can be not performed)
> > > Could somebody explain to me ?
> > >
> > > Tuong Vy
> > > --
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