Re: Rotate two linked proteins against each other and calculate energy profile

From: Ajasja Ljubetič (
Date: Mon Mar 28 2011 - 09:30:28 CDT

 Hi Bjoern,

> I would have taken a detour if you wouldn't have mentioned ABF! Thanks a
> lot
> for this comment!
You're welcome. Actually something similar happened to me when I was
starting out with NAMD. After doing the basic tutorials I browsed through
the manual, but I always skipped the colvars part, because it seem too

So after playing around with NAMD CVS, GBIS, COLVARS, and ABF I could verify
> that my setup works (I just calculated the free energy profile for ethane
> and
> I could reproduce a nice sine like profile for -180 to 180 degree rotation
> with a peak at around 2,7kcal for the eclipsed conformation). Still I have
> some questions how ABF works:
> Why can't I reproduce the above when choosing "lowerBoundary 0" and
> "upperBoundary 360" instead of -180 and 180?
Have you tried setting.
*wrapAround 180*
I don't know about the height difference, it could be due to sampling? How
does the trajectory look in VMD?

> If a bin is poorly sampled, one can interpret this as a highly unfavored
> conformation or the applied force was not sufficient to push the structure
> into this conformation and the process might not be reversible. Is this
> assumption right (assuming that the sampling time was sufficient)?
> Yes, although I'm not sure about the reversibility of the process.

> Is there a built-in keyword which outputs Xi as a function of time
> or can I make NAMD do so in some way.
 If you want the PMF as a function of time check out
If you are interested in the position of the colvar as a function of time,
then you can just plot the colvar trajectory file.

Best regards,

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:50 CST