On 2010-07-15 00.44, Anne Kelley wrote:
I am trying to use GROMACS to calculate the phonons (normal modes) of a bulk
crystal, CdSe. I have found a simple force field, Coulomb + Lennard-Jones, in
the literature (Rabani, J. Chem. Phys. 116, 258, 2002) which the author showed
reproduced the phonon dispersion curves and other mechanical properties of bulk
wurtzite CdSe quite well. A number of other workers have used this force field
in molecular dynamics simulations. But when I use Rabani's force field with
GROMACS I get phonon frequencies that are much too high, up to about 2.2 times
the experimental ones.
I am doing all of my calculations with the double precision version of GROMACS. I have
made a .top file for CdSe using Rabani's Lennard-Jones parameters and ionic charges, and
a .gro file containing an integer number of unit cells with the known lattice constants.
I first do an energy minimization until the maximum forces are around 1.e-4, and get the
right crystal structure and lattice constants. I am using periodic boundary conditions
with PME. I then use the "nm" integrator (with the -t option to read in the
more precise .trr structure file) to calculate the Hessian, and then the g_nmeig_d
program to diagonalize the Hessian and get the normal modes. This all seems to work
fine, but I don't get the literature values for the frequencies (calculated maximum about
450 cm-1, literature and experimental about 215 cm-1). I have checked that when I enter
the correct masses and known harmonic force constant for the H2 molecule, I get back the
right vibrational frequency. I
have tried changing the size of the system (5, 7, or 9 unit cells in each
direction) and it has almost no effect on the frequencies. I have tried things
like changing the Coulomb and Lennard-Jones cutoffs, and even tried regular
Ewald rather than PME (which took a very long time), but these had no
significant effect on my results. I also tried calculating the phonon spectrum
for a different material, AgBr, using a Coulomb + Buckingham potential from the
literature (J. Phys. Chem. 99, 14344, 1995). This gave me a better result, but
still the distribution of frequencies is not correct and the maximum phonon
frequency is about 15% higher than what the authors got with the same force
field.
Are you aware of any issues with GROMACS in doing normal mode calculations on
periodic systems? Can you suggest any likely things I'm doing wrong?
It seems you're doing everything according to the book. Did you double
check the parameter conversions to kJ/mol, nm etc.? Some people write
sigma and epsilon in strange units.
You might want to tighten the ewald_rtol slightly, since you're running
DP anyway, but this should not have a large effect.
Another thing you could play with is manually selecting the FFT grid
spacing to be an integer multiple of the number of unit cells, such that
all the atoms lie on grid points.
Let us know how it goes.
Anne Kelley
Anne Myers Kelley
Professor of Chemistry, School of Natural Sciences
Secretary-Treasurer, APS Division of Laser Science
University of California, Merced
5200 North Lake Road, Merced, CA 95343
Tel. 209-228-4345
amkel...@ucmerced.edu
http://faculty.ucmerced.edu/amkelley/
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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