AMBER Archive (2004)

Subject: AMBER: target rmsd

From: William Andrew McLaughlin (wimclaug_at_popmail.ucsd.edu)
Date: Mon Sep 13 2004 - 15:35:51 CDT

To anyone who may be helpful:

I am trying to use targetted rmsd function for a molecular dynamics
simulation. I would like to vary the rmsd level of the protein backbone
during the simulation and have tried to use the weight function. My
molecular dynamics input file is shown below. As you can see I am trying
to vary the target rmsd from 2 anstroms (value1) down to 0.5 angstroms
(value2). When I run the simulation it appears that the rmsd value does
not vary and just stays at the second value of 0.5 angstrom rmsd. Any
ideas on how to vary the target rmsd for the backbone during the
simulation would be helpful.

Sincerely,

Bill McLaughlin

short molecular dynamics simulation
&cntrl
 imin = 0, ntb = 0,
 igb = 0, ntpr = 100, ntwx = 100,
 ntt = 3, gamma_ln = 1.0,
 tempi = 300.0, temp0 = 300.0
 nstlim = 100000, dt = 0.001, nscm=1,
 cut = 999,
 ntr=1,
 restraint_wt=1.0,
 restraintmask=':2',
 ITGTMD=1,
 tgtrmsmask='@CA,C,O,N,H',
 tgtmdfrc=1,
 tgtrmsd=0.6,
  &wt type='TGTRMSD',istep1=0,istep2=100000,value1=2.0, value2=0.5,
 &wt type='END',
 &end,
/

William McLaughlin, Ph.D.
Dept. of Chemistry and Biochemistry
9500 Gilman Drive
4th Floor Urey Hall
La Jolla, California 92093-0359

Email: wimclaug_at_popmail.ucsd.edu
Phone: (858) 822-4240
Fax: (858) 534-7042

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