[MMTK] Minimization in MMTK2.2b6

Berit Hinnemann Berit.Hinnemann@fysik.dtu.dk
Thu, 13 Sep 2001 18:14:28 +0200


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Dear Konrad,

We are still having problems with the Conjugate Gradient Minimization, I
wrote about some time ago, namely that atoms, for which an attribute
"fixed" is set to one, are not kept fixed. In order to be sure that this
error is not due to an old Python or Numeric version, we now installed
the same versions of Python and Numeric, that you were using

Python-2.1.1 and Numeric 20.1, Redhat 7.1

and I still observe the problem with minimization, that atoms are not
kept fixed.
Now I have a small script minimizing a chain and showing that the atom,
which should not move, moves already in the first step. I have also
tried the Steepest Descent Minimizer, and there the atom is not kept
fixed either.

Could you please try if this script works correctly for you and what you
get as output? The output lines I get are


[0.33599999999999997, 0.56950000000000001, 0.23189999999999997]
Step 0
Potential energy: -54.391430, Gradient norm: 1451.302151
 
Step 1
Potential energy: -83.227165, Gradient norm: 1451.302151
[0.33598936893254117, 0.56921521643713158, 0.23239326994896334]


Thanks a lot,
Berit


-- 
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
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ATOM      1  CH3 ACE A   1      14.295   4.506   3.955  0.00  0.00           C
ATOM      2 HH31 ACE A   1      14.051   3.600   4.551  0.00  0.00           H
ATOM      3 HH32 ACE A   1      14.887   4.213   3.063  0.00  0.00           H
ATOM      4 HH33 ACE A   1      14.887   5.209   4.578  0.00  0.00           H
ATOM      5  C   ACE A   1      13.033   5.169   3.520  0.00  0.00           C
ATOM      6  O   ACE A   1      13.059   6.196   2.844  0.00  0.00           O
ATOM      7  N   GLY A   2      11.836   4.445   3.325  0.00  0.00           N
ATOM      8  O   GLY A   2       9.588   3.012   3.087  0.00  0.00           O
ATOM      9  HA  GLY A   2      10.585   6.065   2.883  0.00  0.00           H
ATOM     10  CA  GLY A   2      10.604   5.169   3.520  0.00  0.00           C
ATOM     11  H   GLY A   2      11.747   3.430   3.239  0.00  0.00           H
ATOM     12  C   GLY A   2       9.429   4.244   3.210  0.00  0.00           C
ATOM     13 3HA  GLY A   2      10.507   5.525   4.561  0.00  0.00           H
ATOM     14  N   GLY A   3       8.233   4.851   3.109  0.00  0.00           N
ATOM     15  O   GLY A   3       5.996   6.286   3.348  0.00  0.00           O
ATOM     16  HA  GLY A   3       6.973   3.231   3.560  0.00  0.00           H
ATOM     17  CA  GLY A   3       7.001   4.123   2.922  0.00  0.00           C
ATOM     18  H   GLY A   3       8.119   5.860   3.225  0.00  0.00           H
ATOM     19  C   GLY A   3       5.834   5.057   3.226  0.00  0.00           C
ATOM     20 3HA  GLY A   3       6.906   3.759   1.884  0.00  0.00           H
ATOM     21  N   NME A   4       4.682   4.364   3.226  0.00  0.00           N
ATOM     22  H   NME A   4       4.646   3.368   3.226  0.00  0.00           H
ATOM     23  CH3 NME A   4       3.430   5.057   3.226  0.00  0.00           C
ATOM     24 HH31 NME A   4       3.360   5.695   2.319  0.00  0.00           H
ATOM     25 HH32 NME A   4       2.598   4.321   3.226  0.00  0.00           H
ATOM     26 HH33 NME A   4       3.360   5.695   4.133  0.00  0.00           H
TER      27      NME A   4
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#!/usr/bin/env python

from MMTK import *
from MMTK.Proteins import PeptideChain, Protein
from MMTK.ForceFields import Amber94ForceField
from MMTK.Minimization import ConjugateGradientMinimizer
from MMTK.PDB import PDBConfiguration, PDBOutputFile 
from MMTK.Trajectory import Trajectory, TrajectoryOutput, LogOutput, StandardLogOutput

universe = InfiniteUniverse(Amber94ForceField())


conf = PDBConfiguration('gly.pdb')

chains = map(PeptideChain, conf.peptide_chains) 
universe.proteins = Protein(chains)
trajectory = Trajectory(universe, "test.nc", "w", "CG on chain")

ouratom=universe.proteins[0][-1].HH31
ouratom.fixed=1

# Minimize
print ouratom.position()
minimizer = ConjugateGradientMinimizer(universe,actions=[TrajectoryOutput(trajectory,("energy",
                                                    "configuration"),0, None, 1),
                                      StandardLogOutput(1)])
minimizer(convergence = 1.e-3, steps = 1)

print ouratom.position()
trajectory.close()


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