[gmx-users] Free energy pertubation

[Alessandra Villa]

Hi Pedro, 

As far I understond, 
the problem could be in the  definition of the bond
interaction for the molecule with MW atom type. 

 "saying multiplicities cannot be perturbed" = it means that 
you are changing (perturbing) the multiplycity of a torsion passing from
state A to state B and this is not possible (see manual p 92 cap 5).
 
Gromacs force field is based on atom type. 
A solution could be to define for each atom of your molecule or for some
of them 
(depend on your system) 
new atomtype (ie CH1 to perCH1) with LJ 0.0 0.0. in the file parameters.
       
in ffgmxnb
   perCH1  0 0.000 A 0.0 0.0
   perN 0 0.000 A 0.0 0.0 
....
in ffgmxbon 
[ bondtypes ]
  CH1   OA    1   0.14300     334720.
  perCH1 perOA 1 0.14300      334720. 

[ dihedraltypes ]
  CH1    N    1   180.000       0.418      6
  perCH1    perN    1   180.000       0.418      6

Best Regards 

alessandra

*******************************************************************************
  Dr. Alessandra Villa		E-mail a.villa at chem.rug.nl
  Biophysical Chemistry        Tel. ++31-50-3634338  Fax. ++31-50-3634800 
  University of Groningen
  Nijenborgh 4
  9747 ag Groningen
  The Netherlands	
*******************************************************************************

On Tue, 20 Aug 2002, Pedro Alexandre Lapido Loureiro wrote:

> Hi Alessandra,
> 
> > So in your *ipt file you have something like this :
> > 
> > ;   nr   type  resnr residue  atom   cgnr     charge       mass  typeB
> > chargeB      massB
> >     1    DUM      1    dum   C65     10       0.0    12.011   C   0.000
> > 12.011 
> > 
> > 
> > where DUM is an atom with zero LJ/charge parameters 
> > 
> > and 
> > does it work?
> 
> Yes, it looks and no it does not work. 
> 
> 
> To begin with I am using the ffgmx forcefield, and so I used the MW atom.
> Grompp complains there are no bond and angle definitions for this atom (I
> created a molecule containing only MW atoms).
> Ok, I can bypass this warnings by increasing the -maxwarn parameter (grompp)
> But then it stops saying multiplicities cannot be perturbed.
> What should I do now?
> 
> Cheers.
> 
> --
> Pedro Alexandre Lapido Loureiro
> Laboratório de Física Biológica
> Instituto de Biofísica
> UFRJ
> Brasil 
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