Re: ABF simulations

From: Sumanth Jamadagni (
Date: Tue Jun 23 2009 - 11:32:43 CDT

Dear Sebastian and NAMD users,

Thanks for your suggestion. I'll try using a larger force constant. But
I was under the impression that the force constants are used primarily
to ensure that the molecule (or group of atoms) stays within Ximax and
Ximin, (within which it remains, but doesn't sample the rest of the
desired reaction coordinate region, just one end) . We have also tried
splitting the region of interest into smaller regions, but the same
problem exists even for much smaller regions (~3 Angstroms).

I am not sure if anybody else if facing the same problem when using zCoord.
Else, we have to go back to umbrella sampling which is what we were
trying to avoid.


Sébastien Légaré wrote:
> Dear Sumanth and NAMD users
> I do not have a final answer to this question but we have had the same
> problem. In most cases, we used a distance reaction coordinate between two
> amino acids in a protein. Since the amino acids are constrained by the rest
> of the protein and do not sample a larger volume at larger distances, I
> suspected that the problem came from a too large Jacobian correction term. If
> you used the zCoord reaction coordinate there is no Jacobian term and I still
> do not see why this happens. You can try setting forceConst to 100
> kcal/mol/Angstroms^2 as suggested in page 3 of Chipot, Hénin, J. Chem. Phys.
> 123, 244906 (2005).
> Regards
> Sébastien Légaré
> On June 9, 2009 10:08:10 pm Sumanth Jamadagni wrote:
>> Dear NAMD users,
>> We have been trying to run some simple ABF simulations to calculate to
>> PMF along z between a molecule and a surface (or similar systems, we
>> have faced the same problem).
>> The problem is this: we specify an /ximax/ and /ximin/ for the reaction
>> coordinate. The center of mass of the molecule initially samples the
>> reaction cordinate and then the molecule is stuck at one end of the
>> reaction coordinate (ximax or ximin) and doesn't diffuse and sample the
>> whole range any more. It therefore accumulates statistics only in the
>> first or last few bins, and there are very few statistics in the rest of
>> the bins. I will try running the sims for much longer to see if that
>> helps, but I suspect I am missing something.
>> Thanks
>> Sumanth Jamadagni
> Sébastien Légaré
> Ph. D. Student
> Laval University
> Quebec, Canada, G1V 0A6
> 418-656-2131 #11577

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