AMBER: Restrained MD (amber9)

From: Vincent Bisetty <>
Date: Tue, 27 Nov 2007 00:52:28 +0200

Dear Users,
    I've done MD simulations under NPT conditions for my small peptide without constraints, and noticed two distribution peaks.
Iam now trying to implement a constraint which is a flat-welled harmonic potential with lower and upper bounds.
In this case lower bound is 120 and upper bound is 240 degrees.

This is my restraining file (disang.rst) used for both the minimization and equilibration runs;

&rst iat= 8, 10, 12, 18, r1=120.0,
r2=120.0, r3=240.0, r4=240.0, rk2=50, rk3=50,
ialtd=0, &end
But it seems like the torsion is still out of range (120-240).
My question is how to get this torsion to move freely within the range 120 and 240, i.e, with No constraint within this range?
Any suggestions will be greatly appreciated.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Nov 28 2007 - 06:07:23 PST
Custom Search