[gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Justin
> 
> In regard to my query regarding the cut-offs at zero with no pbc. I
> assume its is fine to have box dimensions (0 0 0) to comply with the
> definition of a vacuum simulation. I am just worried that there may be
> some default cut-off that I am not aware of.
> 

You have a box of zero size?  That doesn't make any sense to me, and I doubt 
that such a setup plays nice with the MD code.  Frankly, I don't see how it 
worked at all.

What if you place your system in a big box, no PBC, cutoffs = 0, etc?  Does that 
give you a sensible result?

> Cheers
> 
> P.S I have plotted the pullx.xvg files for the distances between the
> COMs of the molecules in the problematic windows. As was the case with
> plotting with g_dist there is significant population of the at the
> extremities of the window compared to that around the average r0.
> 

Then technically, the average is probably fine, so the pull code is satisfied. 
The sampling is clearly messed up for some reason.  Keep digging :)

-Justin

> Justin A. Lemkul wrote:
>>
>> chris.neale at utoronto.ca wrote:
>>> I have seen this before, and there are a few possible reasons, but
>>> I'm still waiting to see that histogram with two peaks
>>> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
>>> It's really hard to help you when we have to guess what the problem
>>> looks like... or perhaps you posted it and I missed it?
>> The histogram was posted several days ago:
>>
>> http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html
>>
>> The attachment link is:
>>
>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin
>>
>>
>> -Justin
>>
>>> -- original message --
>>>
>>> O.K thanks anyway
>>>
>>>
>>> Justin A. Lemkul
>>> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>>>
>>>>
>>>> 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.
>>>>
>>>
> 
> 

-- 
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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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