[gmx-users] van der Walls radius and implicit solvation

Per Larsson per.larsson at sbc.su.se
Tue Jan 11 19:43:11 CET 2011


Currently there is no support in Gromacs for implicit solvation using a united-atom force field.
It is definitely possible though, but you need to consult the literature for values for the radii. 
For united-atoms, I guess the hydrogens you mention are the polar hydrogens?

All radii in the current implementation are taken from the literature, in many cases though using Tinker as the primary source.


11 jan 2011 kl. 19.19 skrev Diogo Vila Viçosa:

> Hi,
> I have two questions regarding the generalized born models implemented in GROMACS.
> 1) Is it possible to perform an MD run using implicit solvent with an united-atom force field? If so, how are determined the van der Walls radii for H atoms?
> 2) How are determined the other van der walls radii used in GROMACS?
> Thanks in advance
> Diogo Vila Viçosa
> -- 
> 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

More information about the gromacs.org_gmx-users mailing list