QwikMD SMD force calculation

From: Aysima Hacisuleyman (ahacisuleyman_at_ku.edu.tr)
Date: Mon Feb 05 2018 - 04:00:02 CST

Dear Namd users,

I’m trying to figure out how QwikMD, advanced analysis plugin calculates
the SMD forces. I’ve checked the distance and force outputs in the log file
but I couldn’t manage to get the output force and distance calculated by
QwikMD. Does anybody know how QwikMD calculates SMD distances and forces? I
know the Jarzynski equation, but It is still not clear whether there is a
unit conversion operation take place during Qwik calculations.


Aysima Hacisuleyman

*Aysima Hacısüleyman*
*PhD Candidate*
*Chemical and Biological Engineering*
*Koc University, Sarıyer, Istanbul, TURKEY*

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