[gmx-users] Free energy pertubation

[Pedro Alexandre Lapido Loureiro]

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