SMD constant velocity not constant

From: Charles Whidborne (charles.whidborne_at_student.adelaide.edu.au)
Date: Wed Oct 29 2014 - 19:25:08 CDT

Hi,

I am doing constant pulling SMD simulations on pulling a small strand of
DNA from another strand by its COM in the -z direction, and constraining
the 'still' strand by a harmonic constraint. I am using the SMD constant
velocity method (config script shown below) at a constant velocity of 5A
per ns over 2ns. However, when i review the simulation, it is infact
pulling initially at a much faster velocity than 5A/ns, initially within
the first 2ps pulls the strand 6A (!!), and then 4A over the next 2ps. Over
the entire simulation the COM of the small strand moves a total of 30A,
instead of the specified 10A.

Is there any explanation as to why this might be occurring? or possibly
something im missing/not doing correctly in my simulation?

SMD on
SMDFile 19-3-trip-0net-10ns.pdb
SMDk 2
SMDVel .000005 ;# 5 A/ns = .005 A/ps = .000005 A/fs
SMDDir 0.00 -1.00 0.00
SMDOutputFreq 200

constraints on
consexp 2
consref 19-3-trip-0net-10ns.pdb
conskfile 19-3-trip-0net-10ns.pdb
conskcol B
selectConstraints on
selectConstrX off
selectConstrY on
selectConstrZ off

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
if {0} {
minimize 10000
reinitvels $temperature
}

run 1000000

Thanks,

Charlie

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