ABF problem with gyration radius/Cl and Br

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Wed Aug 11 2010 - 07:25:41 CDT

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


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