[gmx-users] pbc atom
gmelaugh01 at qub.ac.uk
Tue Aug 24 17:24:27 CEST 2010
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.
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.
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
>> 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:
> The attachment link is:
>> -- original message --
>> O.K thanks anyway
>> Justin A. Lemkul
>>> 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
>>>> 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.
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