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

Thomas Schlesier schlesi at uni-mainz.de
Fri Jul 2 11:39:19 CEST 2010

> 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.


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