AMBER Archive (2003)

Subject: a bug? Re: AMBER: one more line about the npscal, box size changes and rms

From: Dr. Yong Duan (yduan_at_albert.chem.udel.edu)
Date: Thu Aug 07 2003 - 10:49:10 CDT

In the npscal=0, atom-centered scaling, the coordinates of each atom are
scaled. In the npscal=1, the COM of molecules are scaled where the
intra-molecular geometry is unchanged.

In your case, since your protein was kept static, its intra-molecular
forces are not calculated. It actually does not move during regular
coordinate update except at the pressure regulation stage. This should be
changed in the code such that the coordinates of the static part are not
changed during pressure regulation.

yong
On Thu, 7 Aug 2003, Haizhen Zhong wrote:

> Hi there,
>
> I just tried the same system for water-only equilibration and all the
> parameters in .in file are the same except that I set npscal=1. After
> several ps running, the box size is shrinking. Yet the rms between the
> protein from the equilibration and the crystal strucutre is 0.0 and the
> protein looks the same as the crystal.
>
> So why does npscal = 0 or = 1 have such significantly influence on the
> protein
> strucutre? Or is it the difference in how to present the protein between
> npscal = 0 or 1? If it is the presentation problem and not the problem of
> protein itself, is it any way to transform protein structure from npscal =
> 0 to the right structure as those from npscal =1, in order to have the
> right comparison to the crystal structure?
>
>
> Thank you so much!
>
> Haizhen
>
> On Thu, 7 Aug 2003, Haizhen Zhong wrote:
>
> > 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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>
>
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