Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Jan 19 2011 - 06:53:41 CST

Dear all,

>
> If I sampled along two projections (say z and x), do you think that it
> would be possible to obtain the avarage length of the vector in that bin
> without introducing another colvar? The average length in each (x,z) bin
> could probably be obtained from the trajectory in post processing, If the
> DCD is written frequently enough. Or would it be possible do do something
> like this:
>
<write histogram or have a running average of a colvar not in abf>

I'm happy to report that having multiple histogram blocks in addition to
the ABF block works beautifully. At the same time it's also possible to run
the analysis.

One question regarding the *runAveStride:*
Is this the number of steps between two points inside the length window? so
if I have runAveStride 10 and runAveLength 100, then it will only average
ten points?
What I would really like is to output every 100th step the average for the
last 100 steps.

Best regards,
Ajasja

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