[AMBER] steered MD question

From: Baker, Joseph <bakerj.tcnj.edu>
Date: Thu, 23 Jan 2020 15:10:50 -0500

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,

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
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Received on Thu Jan 23 2020 - 12:30:02 PST
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