[gmx-users] dummy atom definition in FEP

[David Mobley]

You don't need virtual sites. That's for something else.

David


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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