AMBER Archive (2000)

Subject: Re: IBELLY

From: Jarrod Smith (jarrod.smith_at_vanderbilt.edu)
Date: Thu Mar 09 2000 - 12:07:13 CST

IBELLY doesn't "freeze" the atoms. I believe what it does is apply a
harmonic constraint to each coordinate. If you watch a trajectory, you will
see the constrained atoms moving with high-frequency vibrations about their
original coordinates.

Jarrod Smith jsmith_at_structbio.vanderbilt.edu
Structural Biology Center Tel: 615-322-1739
Vanderbilt University Fax: 615-936-2211

-----Original Message-----
From: Marios Philippopoulos <mphilip_at_sickkids.on.ca>
To: amber_at_cgl.ucsf.edu <amber_at_cgl.ucsf.edu>
Date: Thursday, March 09, 2000 11:25 AM
Subject: IBELLY

>Does IBELLY really freeze the cartesian coordinates of the specified
>groups during dynamics?
>I just checked the coordinates of the "frozen" atoms in my restart file
>prior to the dynamics run and in the first frame written out in the
>trajectory file, and they differ in the two files. I have two "solute"
>ions in a box of water.
>
>My input file is the following:
>
>---------------------
>
>NpT equilibration of solvent only - 50 ps heating and dynamics
> &cntrl
> imin=0, irest=0, ntx=1, scee=2.0, cut=9.0,
> tempi=0., ntt=1, temp0=300., tautp=0.2,
> ntp=1, taup=0.2,
> ntb=2, ntc=2, ntf=2, ibelly=1, dt=0.002,
> nstlim=50000,
> ntwe=500, ntwx=100, ntpr=25, iwrap=1, ntcm=1,
> &end
>Allow only solvent to move; fix solute atoms:
> RES 3 777
>END
>END
>
>-----------------------
>
>In the output file BELLY seems to be applied to the right atoms:
>
>-----------------------
>........
>LOADING THE BELLY ATOMS AS GROUPS
>
> ----- READING GROUP 1; TITLE:
> Allow only solvent to move; fix solute atoms:
> GRP 1 RES 3 TO 777
> Number of atoms in this group = 2325
> ----- END OF GROUP READ -----
>-----------------------
>
>I have also measured the distance between the two solutes and it has
>changed as well in the course of the trajectory.
>Has anyone else seen this?
>
>Thanks,
>
>Marios Philippopoulos
>
>
>
>
>
>--
>Marios Philippopoulos, PhD
>Structural Biology and Biochemistry Programme
>Hospital for Sick Children
>555 University Avenue
>Toronto Ontario Canada M5G 1X8
>
>mphilip_at_sickkids.on.ca
>
>