[gmx-users] pbc atom

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 24 17:27:41 CEST 2010

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 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.


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