[gmx-users] walls...still struggling
spoel at xray.bmc.uu.se
Sat Nov 8 10:36:01 CET 2003
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.
> Sherwin Singer
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users