Hi,<br>
Thanks for reply. It seems that specifying mass_B = mass_A
doesn't help to solve the problem. However, if I don't use the
directory [virtual_site#] the errors disappear! What's the result if I
do this? Is the directory necessary in the FEP
calculation to define the dummy atoms?<br>
Thanks,<br>
Qin<br><br><div><span class="gmail_quote">On 7/20/07, <b class="gmail_sendername">Stéphane Téletchéa</b> <<a href="mailto:steletch@jouy.inra.fr">steletch@jouy.inra.fr</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;">
Wang Qin a écrit :<br>> Hi there,<br>> I have a problems when I do a FEP calculation.<br>> Below is how I defined dummy atoms in the topology file:<br>> [atom]<br>>
;nr
type resnr
residue atom cgnr charge<br>>
mass type_B charge_B mass_B<br>>
21 opls_172 1
LG6 H21
21 0.4650<br>>
1.00800
opls_0 0.0000 0.000000<br>>
22 opls_172 1
LG6 H22
22 0.4650<br>>
1.00800
opls_0 0.0000 0.000000<br>> ......<br>><br><br>I think you need to specify the mass_B=mass_A, at least this is how it<br>is setup in the tutorials i've done (the one from Berk Hess and the<br>other one from David Mobley).
<br><br>I've also done calculations without setting the mass for B (like you<br>did) and did not encounter any problem, the error you're seing could<br>thus come from another part of your system.<br><br>Cheers,<br>
Stéphane<br><br>--<br>Stéphane
Téletchéa,
PhD. <a href="http://www.steletch.org">http://www.steletch.org</a><br>Unité Mathématique Informatique et Génome <a href="http://migale.jouy.inra.fr/mig">http://migale.jouy.inra.fr/mig</a><br>INRA,
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