[gmx-users] Regarding DUM atom in Gromos force field
mark.j.abraham at gmail.com
Sun Feb 2 18:29:36 CET 2014
On Sat, Feb 1, 2014 at 8:15 AM, bipin singh <bipinelmat at gmail.com> wrote:
> Hello All,
> What is the meaning of the sentence " no idea what the mass should be" in
> atomtype.atp file of Gromos force field.
> "DUM 0.00000 ; dummy atom, no idea what the mass should be. PT3-99"
> Is the mass of of dummy atom is always zero or something else.
What we now call virtual sites in GROMACS were once called dummy atoms, so
it is possible that comment dates from that time.
If during a free energy perturbation some atoms are converted into DUM
> atoms in the B state then how the bonded parameters (bond, angle dihedral)
> will be affected.
I'm no expert here, but if you are making a particle disappear, then its
interactions will have to disappear in a consistent way. You can't have
forces on a particle that has no mass! Doubtless there is literature on the
correct kind of procedure.
> *--------------------Thanks and Regards,Bipin Singh*
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