<br><br><div><span class="gmail_quote">On 7/23/07, <b class="gmail_sendername">David Mobley</b> <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
You don't need virtual sites. That's for something else.<br><br>David</blockquote><div><br>
Thanks a lot for your HELP! <br>
</div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">On 7/23/07, Wang Qin <<a href="mailto:qwang86@gmail.com">qwang86@gmail.com</a>
> wrote:<br>> Hi everyone,<br>>
I am just thinking about if in FEP calculation, I have given the<br>> position information for dummy atoms in the directory of [atoms], do I need<br>> to give the directory [virtual_sites] as well? Since I met a problem when I
<br>> was giving the [virtual_sites] directory and the problem went away when I<br>> 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<br>> type_B charge_B mass_B<br>> 21
opls_172 1
LG6 H21 21 0.4650
1.00800<br>> opls_999 0.0000 1.00800<br>> 22
opls_172 1
LG6 H22 22 0.4650
1.00800<br>> 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>><br>> _______________________________________________<br>> gmx-users mailing list
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