[gmx-users] gromacs: sound wave in liquid?
Dear all, Sorry if my question sounds irrelevant but I am wondering to know if in gromacs there is any tool for studying properties like sound wave/acoustic wave (An acoustic wave is a pressure oscillation that travels through liquid, in a wave pattern)? I dont see such a tool in the manual but I thought maybe someone has an idea how to indirectly extract these information. Please let me know your ideas. Thank you all, Regards, J. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] gromacs: sound wave in liquid?
On Wed, 2011-08-24 at 12:25 -0400, Juliette N. wrote: Dear all, Sorry if my question sounds irrelevant but I am wondering to know if in gromacs there is any tool for studying properties like sound wave/acoustic wave (An acoustic wave is a pressure oscillation that travels through liquid, in a wave pattern)? I dont see such a tool in the manual but I thought maybe someone has an idea how to indirectly extract these information. Please let me know your ideas. Hi, this sounds like a task for a Lattice-Boltzmann code, which is unfortunately not implemented in GROMACS. Moreover as I assume that Coulomb interactions are involved, you perhaps will also get into trouble with momentum conservation, which is hard to achieve with the analytical form of the present SPME. An alternative would be to use the Ewald summation, but this code just runs in serial and for studying sound waves, I assume you need a quite large system, rendering Ewald extremely expensive as it scales with N^(3/2) in the best case. /Flo Thank you all, Regards, J. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] gromacs: sound wave in liquid?
On Wed, 24 Aug 2011 12:25:51 -0400 Juliette N. joojoojo...@gmail.com wrote: Dear all, Sorry if my question sounds irrelevant but I am wondering to know if in gromacs there is any tool for studying properties like sound wave/acoustic wave (An acoustic wave is a pressure oscillation that travels through liquid, in a wave pattern)? I dont see such a tool in the manual but I thought maybe someone has an idea how to indirectly extract these information. Please let me know your ideas. Given that pressure is a bit badly defined in MD simulations, I'd be somewhat skeptical about this. Not to mention the time scales - in order to simulate a sound wave say, at 44 kHz, you'd need to get at least two periods in your simulations, i.e. 45 microseconds, which is a *long* time on the nuclear / MD timescale. -- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.leht...@helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland Jussi Lehtola, FM Tohtorikoulutettava jussi.leht...@helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
