Getting Infinity in Calculation of Free Energy using SMD

From: Ebru Çetin (
Date: Tue Jun 23 2015 - 00:23:19 CDT

Dear NAMD Users,

I am trying to calculate free energy using Jarsynski's equality in steered
MD. I am following Deca-Alanine tutorial and everything goes in well
agreement with the tutorial until free energy calculation. I am using
constant velocity pulling for 10 trajectories as v = 0.01 A/ps and 1 fs/ts.

I am using cumulants script for free energy calculation and after a point
Fexp starts to give INF as result. But the force applied goes 800 pN at
maximum. So, I think work cannot be such a large value to return INF.

Thanks for the help.

Ebru Çetin

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:56 CST