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
Received on Thu Mar 09 2000 - 09:06:06 PST
