[gmx-users] dummy atom definition prob in FEP
Maik Goette
mgoette at mpi-bpc.mpg.de
Wed Aug 8 17:47:40 CEST 2007
Your system will explode.
Actually I'm not sure, why that is, but probably, because some forces
from the bonded terms are transferred to your mass-zero particle, which
then accelerates infinitly fast...even though I would expect some
division over zero error in the velocity calculation...
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:
> 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
> <mailto: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 <http://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>
> > <mailto: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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