[gmx-users] pbc atom

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 24 17:39:59 CEST 2010

Gavin Melaugh wrote:
> O.K Thanks
> My apologies for not stating earlier that I had the box dimensions set
> to zero but I thought that when you set pbc = no and ns_type = simple
> that "ignore the box" (from manual) was implemented.


How many atoms are in your system?  How well-conserved is the temperature?  I 
imagine that if you only have a few atoms (relative to a normal condensed-phase 
system), the species involved would be fairly strongly impacted by the 
(potentially) wide oscillations of the Nose-Hoover thermostat.  Maybe the 
thermostat is kicking your system around?  Check the relevant energies and see 
if they sync up with the configurations moving back and forth.


> Gavin
> Justin A. Lemkul wrote:
>> 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.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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