[gmx-users] Re: g_wham

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 2 12:26:15 CEST 2010

Gavin Melaugh wrote:
> Thanks Justin
> 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?

Nothing has changed as far as I am aware.  Also keep in mind the difference 
between SMD and umbrella sampling.  They are separate procedures, as hopefully 
my tutorial has made clear.


> Gavin
> 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.
>> -Justin
>>> Many Thanks
>>> Gavin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list