ABF atom selection question

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Thu May 05 2011 - 21:50:00 CDT

Dear ABF experts,

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.

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.

Would you please let me know if my understanding is correct?

Many thanks,


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