[gmx-users] ??using pull code when orientation of system changes during MD??

DayleMarieSmith at gmail.com DayleMarieSmith at gmail.com
Wed Jun 3 23:53:09 CEST 2009

Greetings gromacs users--
I'm using the pull code to calculate the binding affinity of a small drug  
molecule to DNA, and I have a concern. Does the pull code (see my pull.ppa  
below) account for the fact that the DNA rotates/translates during MD, and  
therefore the x- y- and z- directions of pulling are changing with time?

verbose = no
runtype = afm
group_1 = drug
reference_group = DNA_site
reftype = com
afm_k1 = 1000

Have a great day,
Dayle Smith

Department of Physics
Whitman College
Walla Walla, WA, USA
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