AMBER Archive (2003)

Subject: AMBER: about the npscal, box size changes and rms

From: Haizhen Zhong (zhongh_at_umich.edu)
Date: Thu Aug 07 2003 - 09:05:08 CDT

Dear Tom and other Amber fellows,

I have one question about npscal. I am using AMBER6.0. According to the
munual, npscal is default set to 0 (atom scaling). Yet when you use this
default, after the NVT ramping (water only, constant volume heating up
from 10 K to
300 K in 30 ps), during the NPT equilibration phase, as the box size
changes from (87, 87, 87) to (74, 74, 74) in an octahedral box, the rms
between the protein in the equilibration phase to the crystal also becomes
bigger and bigger. WHen the system is well equilibrated and the box size
does not change, the rms of protein to the crystal also does not change.

Now my question is: since the first ramping and equilibration is for water
only and only water molecules are in belly for allowable move, therefore
the rms between the protein and the crystal should be 0.0 for any protein
(no matter in the temperature ramping phase, or in the equilibration
phase, since it is only water allowed to move). Yet the npscal = 0 gives
rms = 2.3, is it anything wrong with the protein? Or is it only the
scaling problem during the equilibration due to the change of box size?
When I compare the equilibrated protein to crystal strucutre, I found even
changes in secondary structure of protein occur? Is it right? If it is
because of npscal and scaling problem, what kind of work I have to do to
make the protein in equilibration phase comparable to the crystal (i.e.,
rms=0 for water only)?

By the way, I use Sander_classic in AMBER6, and the protein is about
200 residues. Thank you so much for your
help.
The .in file is as follows,
 &cntrl
    imin=0,
    ntx=7,
    scee=1.2,
    ntb=2,
    ntc=2,
    ntpr=50,
    dielc=1,
    irest=1,
    init=4,
    tempi=300.0,
    ntt=1,
    temp0=300.0,
    tautp=0.2,
    ntp=1,
    ntf=2,
    nstlim=50000,
    ntwe=50,
    ntwx=50,
    dt=.002,
    ndfmin=6,
    jfastw=0,
    nsnb=30,
    cut=12,
    npscal=0,
    ntwr=50,
    ntwv=0,
    ntwxm=0,
    ntwem=0,
    ibelly=1
 &end
Group for belly solvent
RES 206 8202
END
END

Thank you so much,

Haizhen

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