[gmx-users] umbrella histograms

[chris.neale at utoronto.ca]

Gavin,

thank you for plotting the sampling by the time. Looks like this isn't  
a two state problem. Can you also show a histogram image on-list  
please? Just a histogram of the sampled distances.

Thanks,
Chris.

Sorry forgot to attach the files
> Hi Chris
>
> Sorry for the delay. Please find attached a plot of distance between the
> centres of mass of two molecules (also scatter) using umbrella sampling
> at a distance of 2.35 nm. As I said before the g_wham program gives me
> back a histogram with two peaks. I can see from the scatter plot why
> this is the case as there are higher concentrations of point at the
> extremities. What I don't understand is why this behaviour occurs above
> 2nm and not below. I have set all cut-offs to zero and am using no pbc.
>
> Cheers
>
> Gavin
>
> chris.neale at utoronto.ca wrote:
>
>> Your language was not rude, but I did get frustrated after twice
>> asking you to perform an analysis and twice being ignored. My advice
>> still stands: plot the deviation vs. time and report back to the list.
>>
>> Chris.
>>
>> -- original message --
>>
>> Cheers and thanks for the suggestions.
>>
>> P.S. I hope you don't think that the previous msg was in anyway rude. It
>> was actually a genuine question :)
>>
>> Cheers
>>
>> GAvin
>>
>>
>>
>
>

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