If you refer to Justin's tutorial, you can use it for every system,
where the reaction coordinate is the distane between two parts of the
system. You probably need to make some little adjustments, but in the
end it doesn't matter if you pull two proteins apart, or protein+ligand,
2 water molecules, or even streth a protein.
Greetings
Thomas
Am 02.05.2013 08:59, schrieb gmx-users-requ...@gromacs.org:
Sir
I have query as to how to go ahead for potential mean force (PMF)
calculation between protein and ligand. As per the umbrella sampling
protocol you have provided us in gromacs tutotrial it says it is for
protein molecules...
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
