From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 29 2014 - 20:04:28 CDT
On Wed, Oct 29, 2014 at 8:25 PM, Charles Whidborne
<charles.whidborne_at_student.adelaide.edu.au> wrote:
> 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?
how fast the pulled group in SMD moves depends not only on the
velocity but also on the stiffness of the restraint with which the
pulled group is attached to the reference point. if you have a
somewhat soft restraint and your system is moving down a steep
potential, it may run ahead quite a bit untill the restrain limits it.
axel.
>
> 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
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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