[gmx-users] pbc atom

[Gavin Melaugh]

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.

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.
>>>>>
>>>>
>>
>>
>