I am quite sure that I have properly converted sigma and epsilon from the Angstroms and Kelvin given in the paper to nm and kJ/mol. I experimented with changing ewald_rtol from 1e-5 to 1 e-7 while reducing fourierspacing from 0.12 to 0.077, but the effects were negligibly small. The Rabani force field when used in the GULP program generates correct phonon frequencies (thanks to Julian Gale for running this calculation), so there is apparently nothing wrong with the force field.
Any other suggestions? 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/ -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Wednesday, July 14, 2010 11:26 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Phonon calculations in periodic crystals 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
