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

Thomas Schlesier schlesi at uni-mainz.de
Fri Jul 2 12:30:55 CEST 2010

For umbrella sampling you need to steps:
1) get the configurations for the later umbrella sampling (step 5 in 
Justins tutorial). How you perform the pulling sim. for that isn't 
important, you only need the structures.
2) umbrella sampling (step 6 in tutorial). Here you use the 
configurations from step 1. I think here you can only use 
"pull=distance" (i think).


> 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
> analysis?
> Many Thanks
> Gavin
> 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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