SMD pulling speed

From: Charles Whidborne (
Date: Sat Sep 27 2014 - 20:45:48 CDT


I am trying to perform a steered molecular dynamics simulation on a DNA
molecule to pull a small piece of DNA from a longer strand. I have a
pulling speed of 5A per nanosecond, pulling mainly in the x direction and a
harmonic constraint on the longer DNA strand so it doesn't move when pulled
(to allow strand separation). I also have ABF set on the small strand to
measure the PMF because i want the free energy of the separation of the
strands. However, after about 1ns the strand has moved about 20 angstroms
from the initial position, having moved much faster than I expected, the
remainder of the simulation i see a more or less constant pulling of 5A/ns.
Have I done this correctly?
I have also read that during SMD, it is advisable to turn off the langevin
thermostat (possibly replacing it with lowe-anderson) due to dragging
forces on the SMD atom, how do I measure or know that there are dragging
forces on my atom? and can this alter the free energy i'm measuring so that
it gives and incorrect value?

colvars on

SMD on
SMDFile 19-6Trip-1net.pdb
SMDk 2
SMDVel .000005 ;# 5 A/ns = .005 A/ps = .000005 A/fs
SMDDir 1.254 0.229 0.00
SMDOutputFreq 100

constraints on
consexp 2
consref 19-6Trip-1net.pdb
conskfile 19-6Trip-1net.pdb
conskcol B
selectConstraints on
selectConstrX on
selectConstrY off
selectConstrZ off



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