[gmx-developers] Generalized Born

[Per Larsson]

Hi,

11 apr 2009 kl. 19.30 skrev David van der Spoel:

> Hi,
>
> I'm trying to play with the development version of the GBSA code,  
> but documentation is sparse :(. I found the following code in grompp.c

Yes, sorry about that, most of this stuff is till in my head, maybe  
something eventually needs to be on the wiki about how to run GBSA.

>
>
>  have_radius=have_vol=have_surftens=have_gb_radius=have_S_hct=TRUE;
>  for(i=0;i<get_atomtype_ntypes(atype);i++) {
>    have_radius=have_radius       && (get_atomtype_radius(i,atype) >  
> 0);
>    have_vol=have_vol             && (get_atomtype_vol(i,atype) > 0);
>    have_surftens=have_surftens   && (get_atomtype_surftens(i,atype)  
> > 0);
>    have_gb_radius=have_gb_radius && (get_atomtype_gb_radius(i,atype)  
> > 0);
>    have_S_hct=have_S_hct         && (get_atomtype_S_hct(i,atype) > 0);
>  }
>
> this checks whether reasonable numbers have been set. But where  
> should these be specified? In the topology? How?

All GB parameters are included in .itp-files that are specific to each  
forcefield. Currently oplsaa, amber03, amber96 and charmm are  
implemented, but I'm not sure if the actual files are commited to cvs  
yet.

Cheers
/Per