[gmx-users] pbc atom

[Justin A. Lemkul]

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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