[gmx-users] walls...still struggling

[Sherwin J. Singer]

David:

Thanks for your reply!  I just got back into town, so here are the
answers to your questions.

* I have harmonic bonds between O and H of the silanol groups, and a
harmonic Si-O-H angle function.  There is no dihedral around the Si-O
bond.  I agree that the OH could undergo azimuthal rotation around the
Si-O axis, although I would expect non-bonded interactions to make it
less than perfectly free.

* I stayed away from dihedrals, since I thought that would require a
periodic wall or dummy atoms to do that right.  I was trying to get
something simple working, and then build from there.  That is why at the
moment the silanol hydrogens are the only atoms that are not frozen.

* Yes, there are charges on all the wall atoms, both frozen and
un-frozen.  SI atoms have a charge of +.3, OS atoms between silicons
have a charge of -.15.  OA and HO atoms of the silanol groups have
charges of -.475 and .4, respectively.

I am curious why are you asking about the potentials and the charges. 
Even if my model was poorly chosen, wouldn't I still be able to minimize
or cool down the initial configuration?  Would the model cause, for all
groups, the output "Number of degrees of freedom in T-Coupling group ...
is nan"?

I would think that my input of group memberships was the reason that the
silanol H's never minimize or cool down and for the "nan" mentioned
above, but the frozen/unfrozen specification seems to work and visually
ngmx seems to recognize my choice of groups.

Again, help would be very much appreciated.

Regards,
  Sherwin



On Sat, 2003-11-08 at 06:15, David wrote:
> On Sat, 2003-11-08 at 00:53, Sherwin J. Singer wrote:
> > 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.
> How are the H connected? Did you define dihedrals around the Si-O bond?
> Otherwise they have in principle free rotation. Is there water in your
> system? Do you have charges on the Si-O atoms?
> 
> 
> > 
> > * 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.
> > 
> > Thanks,
> >   Sherwin Singer
-- 
Sherwin J. Singer
Department of Chemistry
Ohio State University
Columbus OH, 43214
singer at chemistry.ohio-state.edu
614-292-8909
614-292-1685 (fax)