Hi everyone,<br>
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.<br>
Here is the informaiton from my topology file: <br>
[atoms ]<br>
;nr
type
resnr residue atom cgnr
charge mass type_B
charge_B mass_B<br>
21
opls_172 1
LG6 H21
21 0.4650
1.00800
opls_999 0.0000 1.00800
<br>
22
opls_172 1
LG6 H22
22 0.4650
1.00800
opls_999 0.0000 1.00800<br>
;opls_999 is defined by myself with an atomtype "V" and 0 charge 0 mass<br>
then is this directory necessary?<br>
[virtual_sites3]<br>
;Site from from from funct theta d<br>
21 10
2
1
3 108
0.109<br>
22 11
4
3
3 108 0.109<br>
<br>
I am quite confused. Please help.<br>
<br>
Regards,<br>
Qin<br>
<br>