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

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Jul 2 12:54:26 CEST 2010

O.K Thanks guys


Justin A. Lemkul wrote:
> Thomas Schlesier wrote:
>> 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).
> Both "distance" and "position" work with the WHAM algorithm.  Only
> "direction" is unsupported.  It would be nice for this to be
> officially documented (if it isn't already) so that users don't find
> this out after collecting a huge amount of data that they can't
> analyze.  I know it's on the wiki (I put it there), but a statement in
> the manual is definitely warranted.
> -Justin
>> Greetings
>> Thomas
>>> 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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