[gmx-users] dummy atom definition prob in FEP

[Wang Qin]

Thank you, Maik.
I do want to do standard FEP and thank you for telling me that FEP don't go
with virtual sites. It does help.
BTW, may I ask you why I should define a none_zero mass for a dummy atom?

Thanks,
Qin

On 8/8/07, Maik Goette <mgoette at mpi-bpc.mpg.de> wrote:
>
> Friend...
>
> What are you trying to do???
> If you want to do standard FEP with growing something into dummy (NOT
> virtual site) or from dummy, you must not use virtual sites!
> Virtual sites in fact, have no mass; neither in A- nor in B-state.
> Please read the fManual about virtual particles, their usage and why
> they exist in GROMACS (hint, delocalized charge)....
>
> As far as I know, you can't morph a virtual site to a real particle. I
> also think, It wouldn't make much sense, though.
>
> If you want to morph away e.g. a proton, define a dummy in the b-state,
> which has no LJ parameters (eps and sigma=0) and no charge, but still
> the original mass.
>
> Regards
>
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>          mgoette2[at]gwdg.de
> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
> Wang Qin wrote:
> > Hi,
> >    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?
> >     Thanks,
> > Qin
> >
> > On 7/20/07, *Stéphane Téletchéa* <steletch at jouy.inra.fr
> > <mailto:steletch at jouy.inra.fr>> wrote:
> >
> >     Wang Qin a écrit :
> >      > Hi there,
> >      >         I have a problems when I do a FEP calculation.
> >      >         Below is how I defined dummy atoms in the topology file:
> >      > [atom]
> >      > ;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_0          0.0000  0.000000
> >      > 22      opls_172        1       LG6     H22     22      0.4650
> >      > 1.00800         opls_0          0.0000  0.000000
> >      > ......
> >      >
> >
> >     I think you need to specify the mass_B=mass_A, at least this is how
> it
> >     is setup in the tutorials i've done (the one from Berk Hess and the
> >     other one from David Mobley).
> >
> >     I've also done calculations without setting the mass for B (like you
> >     did) and did not encounter any problem, the error you're seing could
> >     thus come from another part of your system.
> >
> >     Cheers,
> >     Stéphane
> >
> >     --
> >     Stéphane Téletchéa, PhD.                  http://www.steletch.org
> >     Unité Mathématique Informatique et Génome
> http://migale.jouy.inra.fr/mig
> >     INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
> >     78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901
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