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

Mark Abraham 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.

Mark


>
> --
>
>
>
> *--------------------Thanks and Regards,Bipin Singh*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list