[gmx-users] walls...still struggling

Sherwin J. Singer singer at chemistry.ohio-state.edu
Sat Nov 8 00:55:02 CET 2003

I am attempting to simulate a wall consisting of a few layers of
silicate running across system in the xy-plane.  Eventually, the wall
will be in contact with water, but for now I'm trying to just set up
the wall.  The desired results has some similarities to Wensink,
Hoffmann, Apol and Berendsen, Langmuir 16:7392 (2000).

The strategy I took is to make the wall a giant molecule containing
two residues.  The first residue (WALL1) contains inner frozen inner
atoms, and the second residue (WALL2) contains atoms that can move.
To simplify as much as possible now, the moving WALL2 atoms only
include H-atoms of silanol groups (...Si-OH) at the wall surface.  The
WALL1 and WALL2 atoms are identified in an index file, and the total
number of atoms is 4704.

Some things are working right.  Under the "md" integrator the WALL1
atoms are really frozen, and only the WALL2 atoms move.

However, I cannot relax the moving "WALL2" atoms.  I cannot get
conjugate gradient or steepest descents working, and I cannot even
cool down the initial structure by running molecular dynamics with
strong coupling to a thermostat and low temperature.  Those silanol
H's keep flailing violently.

* With steepest descents, I find 

Steepest Descents:
   Tolerance         =  1.00000e+02
   Number of steps   =         1000

Stepsize too small (6.10352e-07 nm)Converged to machine precision,
but not to the requested precision (100)
Steepest Descents did not converge in 15 steps
  Potential Energy  =  1.52274e+08
Maximum force:  2.37367e+02

* With md at 20K, dt=.0005, tcoupl=berendsen, tau_t=.01, ref_t=20, I
generate a trajectory but no apparent cooling even after thousands of
steps.  The following output from grompp makes me think I've done
something wrong.  Please note the "nan" for the number of degrees of
freedom in the T-Coupling groups.

checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1125 of the 1326 non-bonded parameter combinations
Excluding 3 bonded neighbours for WALL 1
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#      BONDS:   1344
#     ANGLES:   1788
initialising group options...
processing index file...
Making dummy/rest group for Acceleration containing 4704 elements
Making dummy/rest group for Freeze containing 448 elements
Making dummy/rest group for Energy Mon. containing 4704 elements
Number of degrees of freedom in T-Coupling group WALL1 is nan
Number of degrees of freedom in T-Coupling group WALL2 is nan
Making dummy/rest group for User1 containing 4704 elements
Making dummy/rest group for User2 containing 4704 elements
Making dummy/rest group for XTC containing 4704 elements
Making dummy/rest group for Or. Res. Fit containing 4704 elements
T-Coupling       has 2 element(s): WALL1 WALL2
Energy Mon.      has 1 element(s): rest
Acceleration     has 1 element(s): rest
Freeze           has 2 element(s): WALL1 rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 2 element(s): WALL1 WALL2
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest

Help would be greatly appreciated.

  Sherwin Singer
Sherwin J. Singer
Department of Chemistry
Ohio State University
Columbus OH, 43214
singer at chemistry.ohio-state.edu
614-292-1685 (fax)

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