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

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Mar 28 2011 - 11:07:43 CDT

Hi Bjoern,

Ajasja has given a good set of answers already, so I'll just add one comment.

> 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)?

If a region is still poorly sampled after a long time, it usually
indicates failure to converge due to slow-relaxing, orthogonal degrees
of freedom - that's the toughest and most common problem. It means
that the choice of colvars is maybe not appropriate for this problem.
Another possible cause is sow diffusion through a very broad region of
colvar space - in this case, splitting that space into windows and
running separate ABF simulations will help a lot.

Best,
Jerome

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