[gmx-users] dummy atom definition prob in FEP

[Wang Qin]

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> 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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