[gmx-users] dummy atom definition in FEP

Wang Qin qwang86 at gmail.com
Mon Jul 23 17:31:34 CEST 2007

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?
;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.

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