Re: ABF atom selection

From: Jérôme Hénin (
Date: Sun May 08 2011 - 11:41:09 CDT

Hi Parisa,

> I am obtaining PMF profile using ABF method (NAMD 2.7 colvar). In "hydration
> free energy calculation for methane" in the tutorial, atom selection is
> defined using atom numbers {1 2 3 4 5}. How this atom selection is different
> from defining only carbon atom number since carbon is the COM for this
> molecule? I am assuming these two are the same.

Almost, but not exactly. Using all atoms to define the group will
collect more data, leading to faster convergence.

> However, if I want to apply force to confine methane movement in XY plane
> (using distance XY), this is not true any more. As I understood, in the
> first case, force is applied to all atoms individually (not COM of these
> atoms) whereas in the second case, force is only applied on the carbon atom.

That is not correct. For both coordinates, you can use either
individual atoms or groups. If a force is "applied to a group" or
"applied to the COM of a group", it means that it is distributed over
all atoms in the group.

Best wishes,

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