[gmx-users] pbc atom

[Justin A. Lemkul]

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.
>>
> 
> 

-- 
========================================

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

========================================