[gmx-users] Mass in GMX topology

[Dr. Vitaly Chaban]

On Thu, Jul 11, 2013 at 1:17 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Thank you. Another question: Does RDF depends on the mass of the atom? On
> the one hand it gives different value of the force in equation of motion
> but on the other hand velocities are rescaled with a thermostat.
>
>

It does not. Provided that ergodicity applies to your calculation/system.

No different value of the force, just of the acceleration.


Dr. Vitaly V. Chaban






> Steven
>
>
> On Thu, Jul 11, 2013 at 12:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 7/11/13 7:54 AM, Steven Neumann wrote:
> >
> >> Dear Users,
> >>
> >> Can you please write me where gromacs does read the mass of each atom:
> Is
> >> that the [atoms] under [moleculetype] or from [atomtypes] ? I wish to
> >> assign different mass for two different beads of the same type in my
> >> topology.
> >>
> >>
> > It is taken from [atoms].  The entries for mass in [atomtypes] are only
> > used if the mass field is blank in the [atoms] directive, IIRC.  Easy to
> > check, of course, with gmxdump :)
> >
> > -Justin
> >
> > --
> > ==============================**====================
> >
> > Justin A. Lemkul, Ph.D.
> > Postdoctoral Associate
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
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> > 20 Penn St.
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> >
> > jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu>
> | (410)
> > 706-7441
> >
> > ==============================**====================
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