No, belly does not use restraints. That is done using the NTR option, which
restrains the positions of atoms. The belly option zeroes the forces on the
atoms,
but they can still move, especially if you are using constant pressure
simulation.
In that case they are movewhen all coordinates are scaled when the box volume is
adjusted.
Jarrod Smith wrote:
> 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>
> 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
> >
> >
--
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336 NOTE NEW AREA CODE
Department of Chemistry Fax: (631) 632-7960
SUNY at Stony Brook Web: http://morita.chem.sunysb.edu/carlos
Stony Brook, NY 11794-3400 E-mail: csimmerling_at_sbchem.sunysb.edu
===================================================================
Received on Thu Mar 09 2000 - 10:43:44 PST
