From: Charles Whidborne (charles.whidborne_at_student.adelaide.edu.au)
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?
SMDVel .000005 ;# 5 A/ns = .005 A/ps = .000005 A/fs
SMDDir 1.254 0.229 0.00
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