[gmx-users] umbrella sampling (PMF) position discrepancy

Raphael Alhadeff raphael.alhadeff at mail.huji.ac.il
Tue Oct 2 15:15:16 CEST 2012

Hello Gromacs users,

The solution that ended up working is selecting a different pull_pbcatom0
from the reference group, the protein, such that the atom is approx. in the
center of mass of the protein.

I hope that others may find this useful,

Thanks to Martin Vesper and Justin Lemkul for their insights,


On Tue, Sep 11, 2012 at 5:22 PM, Raphael Alhadeff <
raphael.alhadeff at mail.huji.ac.il> wrote:

> Thank you all for your help,
> Sheeba-
> Yes, I get both positive and negative results. I think what you describe
> is what I would get if I used 'distance' for the geometry.
> In any case, I have values from +2 to about -3, and they are not evenly
> distributed (unlike the coordinates, which are more or less evenly
> distributed) but are rather highly packed around -1 and then get
> increasingly farther away from each other.
> Jianguo-
> I did not see that thread before, I read it now but could not find
> anything to solve my problem.
> Justin-
> Thank you very much for your willingness to help, I will send the files
> promptly.
> Thanks again to everyone, I will post again should we find the problem and
> solution for anyone who might find it useful..
> Raphael

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