[gmx-users] walls...still struggling (not)
David van der Spoel
spoel at xray.bmc.uu.se
Mon Nov 24 11:05:01 CET 2003
On Mon, 2003-11-24 at 10:52, Sherwin J. Singer wrote:
> I can report 1) a problem solved, and 2) unexpected behavior
> concerning genbox input options.
>
> 1) I've written recently about constructing flexible silanol groups on
> an otherwise frozen silicate wall. Gromacs md would move the silanol
> oxygens and hydrogens, but would claim the kinetic energy was zero,
> gave "nan" for the number of degrees of freedom, and would not
> thermostat or energy minimize the structure.
>
> My problem turned out to be the center of mass constraints. I had
> given the two groups for center of mass removal as "comm_grps = WALL1
> WALL2", where the WALL1 group is frozen, and WALL2 is the silanols.
> When I simply specify "comm_grps = SYSTEM", all is well. I'm not sure
> why removing 3 center of mass degree of freedom among 448 silanol
> atoms messed me up, but it did.
thanks for the report.
>
> 2) I then went to solvate my wall.
> "genbox -cp walls_run1.gro -p walls.top" added 0 waters, while
> "genbox -cp walls_run1.gro -cs spc216.gro -p walls.top" added 9180
> waters. Isn't spc216.gro the default for the -cs option?
>
yes, but you still have to give the -cs option, otherwise the behaviour
of the program is different.
> Regards,
> Sherwin Singer
>
>
> On Wed, 2003-11-12 at 03:31, David van der Spoel wrote:
> > On Wed, 2003-11-12 at 00:30, Sherwin J. Singer wrote:
> > > 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.
> > >
> > OK, check the rotation anyway once you get it going.
> >
> > > * 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"?
> > >
> > The number of DOF for a group is computed from 3*natoms - Nconstr. Now
> > if the atoms are frozen, the nDOF is zero, it may be that something is
> > divided by zero somewhere. Check what it says in your tpr file. You
> > might actually consider to let the oxygens fluctuate as well, or, for
> > debugging purposes, to make the OH bond a flexible one.
> >
> >
> > > 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
--
David.
________________________________________________________________________
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
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