Thank you, Maik.<br>
I do want to do standard FEP and thank you for telling me that FEP don't go with virtual sites. It does help.<br>
BTW, may I ask you why I should define a none_zero mass for a dummy atom? <br>
<br>
Thanks,<br>
Qin<br><br><div><span class="gmail_quote">On 8/8/07, <b class="gmail_sendername">Maik Goette</b> <<a href="mailto:mgoette@mpi-bpc.mpg.de">mgoette@mpi-bpc.mpg.de</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;">
Friend...<br><br>What are you trying to do???<br>If you want to do standard FEP with growing something into dummy (NOT<br>virtual site) or from dummy, you must not use virtual sites!<br>Virtual sites in fact, have no mass; neither in A- nor in B-state.
<br>Please read the fManual about virtual particles, their usage and why<br>they exist in GROMACS (hint, delocalized charge)....<br><br>As far as I know, you can't morph a virtual site to a real particle. I<br>also think, It wouldn't make much sense, though.
<br><br>If you want to morph away e.g. a proton, define a dummy in the b-state,<br>which has no LJ parameters (eps and sigma=0) and no charge, but still<br>the original mass.<br><br>Regards<br><br>Maik Goette, Dipl. Biol.
<br>Max Planck Institute for Biophysical Chemistry<br>Theoretical & computational biophysics department<br>Am Fassberg 11<br>37077 Goettingen<br>Germany<br>Tel. : ++49 551 201 2310<br>Fax : ++49 551 201 2302<br>Email : mgoette[at]mpi-
<a href="http://bpc.mpg.de">bpc.mpg.de</a><br> mgoette2[at]gwdg.de<br>WWW : <a href="http://www.mpibpc.gwdg.de/groups/grubmueller/">http://www.mpibpc.gwdg.de/groups/grubmueller/</a><br><br><br>Wang Qin wrote:<br>
> Hi,<br>> Thanks for reply. It seems that specifying mass_B = mass_A doesn't<br>> help to solve the problem. However, if I don't use the directory<br>> [virtual_site#] the errors disappear! What's the result if I do this?
<br>> Is the directory necessary in the FEP calculation to define the dummy<br>> atoms?<br>> Thanks,<br>> Qin<br>><br>> On 7/20/07, *Stéphane Téletchéa* <<a href="mailto:steletch@jouy.inra.fr">
steletch@jouy.inra.fr</a><br>> <mailto:<a href="mailto:steletch@jouy.inra.fr">steletch@jouy.inra.fr</a>>> wrote:<br>><br>> 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, Domaine de
Vilvert Tél
: (33) 134 652 891<br>> 78352 Jouy-en-Josas
cedex, France Fax :
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