[gmx-users] pbc atom

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 24 15:40:44 CEST 2010

Gavin Melaugh wrote:
> For the umbrella sampling I am not pulling in any direction I am just
> applying the umbrella potential so that two molecules can sample space
> about a give value of r0 (COM distance). Maybe I am confused but should
> I not plot the absolute value of the displacement (modulus) as supposed
> to the displacement along a given vector component?

For diagnosing weird behavior, I would always start with the primary data, not 
any post-processed interpretation of it.  Use the pullx.xvg file.  Any weird 
changes in sign or sudden changes in magnitude would indicate problems.  If you 
start manipulating the data, you may be hiding the real reason for the problem.


> Gavin
> Justin A. Lemkul wrote:
>> Gavin Melaugh wrote:
>>> I always used g_dist to plot the COM distances because the pullx.xvg
>>> files doesn't give this value directly. Can you access the COM distance
>>> from the pullx.xvg file
>> That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference
>> group, then displacement (dX,dY,dZ) of the pull group relative to the
>> reference.  Not all terms may be present, depending on the axis along
>> which you're pulling, i.e. if you only pull along Z, there will be two
>> terms in pullx.xvg - Z and dZ.
>> -Justin
>>> Gavin
>>> Justin A. Lemkul wrote:
>>>> Gavin Melaugh wrote:
>>>>> Justin
>>>>> I have looked at the movies but it's very hard to tell what's going on
>>>>> as I save teh trajectories every 250000 steps for every 50000000 step
>>>>> simulation (100 ns). Ill look at them  again in more detail and post
>>>>> back.
>>>> Plotting the pullx.xvg file(s) may be useful, too, to indicate where
>>>> any weird jumps or sudden changes in position might occur.  Mapping
>>>> that information back onto the trajectory could help focus your
>>>> attention.
>>>> -Justin
>>>>> Gavin
>>>>> Justin A. Lemkul wrote:
>>>>>> Gavin Melaugh wrote:
>>>>>>> O.K thanks anyway
>>>>>> I saw the plots you posted during a conversation with Chris, but I'll
>>>>>> ask the obvious anyway: have you watched the trajectories for any of
>>>>>> the problematic windows?  It didn't seem like you had two metastable
>>>>>> states, but maybe having a look at the movie would shed some light on
>>>>>> what's going on.  I know that's the first thing I'd do.
>>>>>> -Justin
>>>>>>> Justin A. Lemkul wrote:
>>>>>>>> Gavin Melaugh wrote:
>>>>>>>>> Thanks Justin
>>>>>>>>> Have you any idea why when generating umbrella histograms for the
>>>>>>>>> pmf I
>>>>>>>>> would get two peaks in the histograms above a distance of 2 nm,
>>>>>>>>> but
>>>>>>>>> below 2 nm I get well behaved histograms that lead to a very
>>>>>>>>> good profile in the pmf. To the best of my knowledge the
>>>>>>>>> configurations
>>>>>>>>> are all very well equilibrated at their respective COM distances.
>>>>>>>>> Umbrella sampling is performed on all windows using a force
>>>>>>>>> constant of
>>>>>>>>> 1000 kj/mol at 600 K.
>>>>>>>> Sorry, no clue.
>>>>>>>> -Justin
>>>>>>>>> Cheers
>>>>>>>>> Gavin
>>>>>>>>> Justin A. Lemkul wrote:
>>>>>>>>>> Justin A. Lemkul wrote:
>>>>>>>>>>> Gavin Melaugh wrote:
>>>>>>>>>>>> Hi all
>>>>>>>>>>>> I am generating a series of configurations using the pull
>>>>>>>>>>>> code to
>>>>>>>>>>>> calculate the pmf. I am using no pbc i.e. pbc =no, howver the
>>>>>>>>>>>> output
>>>>>>>>>>>> from grommp gives me info on pbc atom.
>>>>>>>>>>>> Pull group  natoms  pbc atom  distance at start    
>>>>>>>>>>>> reference at
>>>>>>>>>>>> t=0
>>>>>>>>>>>>        0        72        36
>>>>>>>>>>>>        1        72       360   4.290                 4.290
>>>>>>>>>>>> why is this so?
>>>>>>>>>>> grompp always assigns the numerical middle atom of a group as
>>>>>>>>>>> the
>>>>>>>>>>> PBC 
>>>>>>>>>> ...unless over-ridden by providing a different value for
>>>>>>>>>> pbc_pullatom1.
>>>>>>>>>> -Justin
>>>>>>>>>>> reference point.  In the case of pbc=no, it shouldn't matter.
>>>>>>>>>>> http://manual.gromacs.org/current/online/mdp_opt.html#pull
>>>>>>>>>>> -Justin
>>>>>>>>>>>> Cheers
>>>>>>>>>>>> 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