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

[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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