[gmx-users] pbc atom

[Justin A. Lemkul]

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
>>>
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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