[gmx-users] pbc atom

[Gavin Melaugh]

There are 168 atom types in my system, 2 molecules comprising of 84
atoms each. The average temperature is 600 K but there are large
fluctuations ca ~100 K, which I assume is expected with such a smal
system. Ill check the energies

Gavin

Justin A. Lemkul wrote:
>
>
> 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.
>>
>
> Indeed.
>
> 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.
>
> -Justin
>
>> 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.
>>>>>>>
>>>>
>>
>>
>