AMBER Archive (2003)

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

From: Haizhen Zhong (zhongh_at_umich.edu)
Date: Thu Aug 07 2003 - 12:54:17 CDT

Hi there,

Thanks to Yong and Andy's prompt reply.

According to my understanding from these two reply, it seems it's better
to use
npscal=1 rather than npscal=0. Since npscal = 0 is default value, there
may be some reason to use npscal=0 in certain cases and in other cases, it
may be better to use npscal=1. Now my new question is:

"Are there some rules that define when is it best to use npscal=0 and when
to use npscal=1? Is there any guideline in the manual?"

Or according to Yong's indication, is there a bug when npscal is set to 0?
In such case, does it mean not to use npscal = 0 at all?

Thank you so much!

Haizhen

>
> 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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