[gmx-users] Regarding DUM atom in Gromos force field

[Mark Abraham]

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.

Mark


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