Extra bonds-ABF

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Mon Nov 07 2011 - 10:53:18 CST

Dear NAMD experts,

I need to use "extra bond" in ABF calculations to keep the distance between two atoms fixed. In the manual it says "the energies from extra bonded terms are included with the normal bond, angle and dihedral energies in NAMD output". I am wondering if this means the K value I use as the spring constant affects the results of force calculation by ABF? If so, is there any way to know the contribution of the "extra bond" force in ABF output force separately?



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