If that's the case, I don't see the difference with NTR.
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
> >
> >
--
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
Received on Thu Mar 09 2000 - 10:09:49 PST
