How to restraint pairinteractions

Date: Wed May 30 2012 - 17:01:20 CDT

Dear NAMD users,

I am trying to run NAMD simulation to generate the PMF with
pairinteractions as a reaction coordinate.
One way to do this is to use the colvar module in NAMD, umbrella sampling
followed by WHAM. Unfortunately, in terms of the user guild of NAMD,
pairinteraction is not the predefined colvar in NAMD.

Therefore, I am wander if this can be done by using the user defined force
(tclforce). But I don't know how. Could you please let me know whether you
have any suggestions to solve this issue?



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