Re: ABF problem with gyration radius/Cl and Br

From: Jérôme Hénin (
Date: Wed Aug 11 2010 - 08:31:44 CDT

Hi Branko,

It is not clear to me what the problem is. What tells you that the
results are incorrect? Is the sampling well-distributed in all cases?
(I would be surprised, simply because it is hard to sample a 3D domain
well with ABF)
Also, I don't think I will be able to help unless I see a sample
rendering of the data showing the incorrect behavior.


On 11 August 2010 14:25, Branko <> wrote:
> Dear ABF developers,
> I have 3D PMF calculated for 25 molecules in explicit solvent, 20 ns each.
> Calculation was performed using 2.7b2. Same colvar combinations were used
> for each molecule. One colvar is always gyration radius of specified atoms.
> For all molecules having Cl or Br (included in “gyration atoms”), within
> set, 3D PMF plot is “shifted out” from predefined boundaries, in a way that
> minima were positioned at the upper edge of boundary. Values of boundaries
> are chosen from previous 20 ns run and confirmed by the calculation of the
> radius of gyration of chosen atoms on the finished trajectory (same one from
> which PMF was derived). From molecules comprising only C, O, S and H same
> problem does not exist. First question is: are someone observe similar
> problem, second question is what should I do to overcome the problem. Thanks
> a lot in advance.
> Branko

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:24 CST