[gmx-users] best parameters for energy determination with GBSA
per.larsson at sbc.su.se
Thu Oct 7 12:57:31 CEST 2010
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.
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
> -pd ; in mdrun
> Then, there are the implicit solvent parameters themselves:
> gb_algorithm= Still
> 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):
> -d 5.0 ; in editconf
> What do you say?
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