gmelaugh01 at qub.ac.uk
Fri Jul 2 11:35:33 CEST 2010
Is it possible to use g_wham with pull_geometry = direction, I read on
the website that you couldn't but was wondering if this had changed?
Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> Hi All
>> I am using COM pulling to pull two molecules together in order to
>> calculate the potential of mean force and the pulling is fine. I am
>> using pull = umbrella for the pulling as I am following
>> the tutorial on the website. If I use pull = constraint does this still
>> pull the molecules together, and if so do you still then need to
>> perform umbrella sampling on the configurations generated? I am a little
>> confused as I don't understand how the molecules pull together if they
>> are constrained.
> For plain SMD, you can use any of the pull methods. In the tutorial I
> wrote, I explain why I used "pull = umbrella" during SMD. Umbrella
> sampling is a separate procedure, which can be done after SMD. If you
> want a free energy along the reaction coordinate, there are several
> methods for doing this, among which is umbrella sampling.
>> Many Thanks
More information about the gromacs.org_gmx-users