SMD of small molecule dimer

From: dora guzman (
Date: Fri Apr 28 2006 - 12:05:39 CDT

I'm currently using NAMD to run SMD of a small dimer molecule. I'm using
the constant velocity pulling method to calculate the force necessary to
pull the two fragments apart, which are only interacting via 6 hydrogen
bonds. I would expect that once the hydrogen bonds between the two
fragments are ruptured, the force that was built up should rapidly
decrease to zero. However, I don't see this happening when analyzing the
force-extension curve. Even when the two fragments are very far apart
the force does not decrease significantly. Am I calculating the force
correctly? I'm using the same procedure in the tutorial,

cat filename.log | awk '{if ($1=="SMD") print $0}'> smd.dat


cat smd.dat | awk '{print $6*nx + $7*ny + $8*nz}'> ft.dat (and the same
for calculating extension using columns 3-5)

Any advice would be greatly appreciated.


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