[MMTK] Re: Conjugate gradient minimization in 2.2b6

Berit Hinnemann Berit.Hinnemann@fysik.dtu.dk
Mon, 20 Aug 2001 11:19:06 +0200


Konrad,

I am running MMTK on a PC with Redhat 7.1. The versions are Python-1.5.2
and Numeric-17.3.0.
I ran your script on my outfile "gly_allCH3.nc" and it only printed "0"
which of course explains what I had observed.

There's one thing I don't understand, namely how the atoms are numbered.
Is the numbering according to the list you get with
"universe.atomList()? When I create a universe from "gly.pdb", then I
get

universe.atomList()[0] = Atom .chain1.ACE1.CBond
universe.atomList()[22] = Atom .chain1.NME4.HH31
universe.atomList()[26] = Atom .chain0.ACE1.CBond
universe.atomList()[48] = Atom .chain0.NME4.HH31

which are not the atoms which get an attrobute "fixed" in the script.
Also, if the numbering is according to the input pdb-file, it is the
wrong atoms. 

Thank you,
Berit

Konrad Hinsen wrote:
> 
> > I am trying to do conjugate gradient minimization with fixed atoms, now
> > with the beta version of MMTK, 2.2b6, and I encounter the same problems
> > as I described in an earlier email.
> 
> I just checked it with my installation, and it works as it should.
> Here's a script to check the trajectory:
> 
>    from Scientific.IO.NetCDF import NetCDFFile
>    from Numeric import *
> 
>    t = NetCDFFile('gly_allCH3.nc')
> 
>    conf = t.variables['configuration'][:]
>    natoms = conf.shape[1]
> 
>    for i in range(natoms):
>        at = conf[:, i, :]
>        equal_values = add.reduce(add.reduce(equal(at, at[0:1])))
>        if equal_values == multiply.reduce(at.shape):
>            print i
> 
>    t.close()
> 
> It prints the indices of all atoms that don't move, not even using MMTK,
> so I am not cheating ;-)  Here's what it prints for me:
> 
>    0
>    22
>    26
>    48
> 
> What system are you running this on? What versions of Python/NumPy
> do you use?
> 
> Konrad.
> --
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-- 
Berit Hinnemann
Center for Atomic-Scale Materials Physics (CAMP)
Dept. of Physics, Technical University of Denmark
Building 307, DK-2800 Lyngby, Denmark 
Phone: +45 4525 3209, Fax: +45 4593 2399