[gmx-users] best parameters for energy determination with GBSA

[Per Larsson]

Hi Ehud!

Your settings are correct.
However, you can also use domain decomposition with GB,
and I at least usually bypass the editconf stage, and do pdb2gmx->grompp->mdrun, when you do not want any pbc.

/Per



7 okt 2010 kl. 12.29 skrev Ehud Schreiber:

> Dear GROMACS users,
>  
> I try to compute energies of a small peptide-domain complex and of its constituents using implicit solvent, so that I can get the binding Delta E. I need the accuracy to be high enough so that I can reliably measure the Delta Delta E between the wildtype peptide and a mutation of it.
>  
> I would like to get advice as to the best setting and parameters to use; are the ones given below the correct and best ones (most in an mdp file, some run control parameters of GROMACS commands)? Are other defaults in need to be changed?
>  
> As the GBSA method necessitates using the inexact cut-off interactions, and my system is rather small, I consider using no cut-off at all, i.e. an all-vs.-all approach. For that I understand the parameters should be
> nstlist=0
> ns_type=simple
> -pd ; in mdrun
> coulombtype=cut-off
> rcoulomb=0
> vdwtype=cut-off
> rvdw=0
> rlist=0
>  
> Then, there are the implicit solvent parameters themselves:
> implicit_solvent=GBSA
> gb_algorithm= Still
> sa_algorithm=Ace-approximation
> rgbradii=0
>  
> Finally, regarding the simulation box, I see no need for periodic boundary conditions, and I pick some big margin around the system (as there are no water molecules, no need to spare):
> pbc=no
> -d 5.0 ; in editconf
>  
> What do you say?
>  
> Thanks,
> Ehud.
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