[gmx-users] dummy atom definition in FEP

[Wang Qin]

On 7/23/07, David Mobley <dmobley at gmail.com> wrote:
>
> You don't need virtual sites. That's for something else.
>
> David


Thanks a lot for your HELP!

On 7/23/07, Wang Qin <qwang86 at gmail.com> wrote:
> > Hi everyone,
> >           I am just thinking about if in FEP calculation, I have given
> the
> > position information for dummy atoms in the directory of [atoms], do I
> need
> > to give the directory [virtual_sites] as well? Since I met a problem
> when I
> > was giving the [virtual_sites] directory and the problem went away when
> I
> > deleted it, I want to make sure if what I did is right.
> >          Here is the informaiton from my topology file:
> >   [atoms  ]
> >  ;nr     type            resnr   residue atom    cgnr    charge  mass
> > type_B  charge_B        mass_B
> >      21   opls_172      1 LG6      H21      21    0.4650       1.00800
> >     opls_999        0.0000  1.00800
> >      22   opls_172      1 LG6      H22      22    0.4650       1.00800
> >     opls_999        0.0000  1.00800
> >  ;opls_999 is defined by myself with an atomtype "V" and 0 charge 0 mass
> >  then is this directory necessary?
> >  [virtual_sites3]
> >  ;Site from from from funct theta d
> >  21      10      2       1       3       108      0.109
> >  22      11      4       3       3       108     0.109
> >
> >           I am quite confused. Please help.
> >
> >  Regards,
> >  Qin
> >
> >
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