Hi all,
I am running some directional pulling simulations of some filament proteins
using the jar=1 option in amber and fxyz=0,0,1 (filament axis aligned with
the z-direction). My igr1 and igr2 selections in the DISANG file define
some center of mass groups that I am pulling between. In my main simulation
input file in the &cntrl block I am also putting a light restraint on the
igr1 atoms (0.5 kcal/mol/A^2) to prevent rotation of the filament in the
long rectangular water box. Things seem to be working well (no system
crashes or anything like that). I am wondering if there are any subtleties
that I should be aware of in terms of analyzing the force vs extension data
in a simulation that uses both steered MD and light positional restraints
on some of the atoms? Thanks for your comments.
Kind regards,
Joe
------
Joseph Baker, PhD
Associate Professor
Department of Chemistry
C212 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: http://bakerj.pages.tcnj.edu/
Pronouns: he/him/his
Chair/Chair-elect (2019), Trenton Local Section of the ACS
Chemistry Division Councilor (2018-2021), The Council on Undergraduate
Research
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Received on Thu Jan 23 2020 - 12:30:02 PST
