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

[bipin singh]

Thanks Dr. Mark for your reply.

My doubt is when we convert some atoms to a dummy atom (DUM) in a B state
topology, then does the Gromacs free energy code automatically take care of
this transformation in bonded terms (bond, angle, dihedral etc.) because we
can not define B state parameters corresponding to bonded terms of dummy
atoms in a topology.

Another doubt is what would be the option need to be set in mdp file for "
*couple-lambda1*" when we do free energy perturbation through B state
topology:

For example:

At lambda=0, I have to use:
couple-lambda0 vdw-q (all interactions are on at lambda=0 )

At lambda=1.0, I am not sure what should be the correct option:
couple-lambda1 none; I think none will not work here since I am selectively
turning off vdw and charges for few atoms by changing it to dummy atom in B
state topology.




On Sun, Feb 2, 2014 at 10:58 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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*
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-- 



*--------------------Thanks and Regards,Bipin Singh*