[gmx-users] dummy atom definition prob in FEP

[Maik Goette]

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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