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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