VMD-L Mailing List

From: Charles Whidborne (charles.whidborne_at_student.adelaide.edu.au)
Date: Mon Aug 04 2014 - 19:36:33 CDT

Hi,

I am running simulations on DNA in which i have equilibrated it over so
many nanoseconds and now i want to measure the free energy of separating
the strands using adaptive biasing force (ABF) in NAMD, but due to my
inexperience (and probably lack of understanding) i am having trouble
running the simulation successfully. I have done the ABF tutorials but they
dont seem to help much when I try to relate it to my problem.

In my NAMD config file i have:
colvars on
colvarsConfig Distance.in