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

Per Larsson per.larsson at sbc.su.se
Thu Oct 7 12:57:31 CEST 2010

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.


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.
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101007/2fe549be/attachment.html>

More information about the gromacs.org_gmx-users mailing list