[gmx-users] Re: another pull-code question

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Jul 2 11:55:31 CEST 2010

Thanks Thomas

That has made things a lot clearer, but just to be sure. If I pull the
molecules using pull = constraints, do I still have to run umbrella
sampling on the generated configurations in order to calculate the PMF?
Also if I use pull_geometry = direction for the pulling can I use it for
the umbrella sampling with the intention of then using g_wham for the

Many Thanks


Thomas Schlesier 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
> Some additions to Justins comment:
> If you want to perform the umbrella sampling (or calculating the pmf
> form integrating the constraint forces) it doesn't really matter how
> you obtain the structures for the different windows (but you will need
> them).
> If you only want to perform the calculating of the pmf,
> "pull=constraint" it's a little easier to get these structures. You
> can perform your pulling so that each frame of the trajectory
> correspondents to one structure and then extract them from the .trr /
> .xtc. Also the pulling velocity doesn't really matter. If you pull
> with 1nm/ns and save the coordinates every ns, then the distance of
> your molecules will increase/decrease with 1nm between the different
> frames.
> If you use the same setup with "pull=umbrella" the change of the
> distance won't be 1nm but will depend on "pull_k1" the spring constant
> with which you're pulling. So you must "search" the structures with
> the right distances (for that is Justin's Perl script).
> The nice thing with "pull=umbrella" is that you can see qualitativly
> what happens during the pulling. If there is somewhere a barrier in
> the pmf you will see it (more or less) that the distance between the
> two molecules will change slower then if the is no barrier. With lower
> velocity and spring constant (pull_k1) you will see that better.
> But with "pull=constraint" you won't see that. Think the best way to
> understand the difference between "pull=umbrella" and "=constriant" is
> that the later is the first in the limit of an infinte "pull_k1".
> Hope that helps. Good thing could be, take a small test system and
> play around with the parameters and look what happens.
> Greetings
> Thomas

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