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<br><br>> From: makoto-yoneya@aist.go.jp<br>> To: gmx-users@gromacs.org<br>> Date: Mon, 10 Jan 2011 23:57:46 +0900<br>> Subject: [gmx-users] truncated LJ potential<br>> <br>> Dear David and Hess:<br>> <br>> Thanks a lot for quick replies.<br>> <br>> >> please look into gromacs' table potential functionality, it is described <br>> >> in the manual, and you won't have to program anything<br>> >> UNLESS the sigma is different for different atom pairs, in that case I'm <br>> >> not sure if it will work.<br>> <br>> The target system has many different atom types with different sigmas (and<br>> epsilons).<br>> I'd like to switch between the standard LJ potential simulation and the<br>> corresponding<br>> repulsion only one with the same LJ parameter sets for the real compounds<br>> not simplified models.<br>> <br>> > You can make different tables for interactions between groups of atoms<br>> with<br>> > different sigma's by putting these groups in different energy groups,<br>> > but this might get tedious.<br>> <br>> As the modification which I'd like to try is very simple one from the <br>> original LJ function, I'd like to try to modify the code instead of<br>> supplying<br>> many kinds of the tables for each pairs of atom types.<br>> <br>> > You can also set the environment variable nb_generic.c and modify<br>> > src/gmxlib/nonbonded/nb_generic.c, but might lead to somewhat<br>> > slower simulations.<br>> <br>> The LJ potential and force code in the above looks like in the c6-c12 form<br>> not in epsilon-sigma one.<br>> The LJ potential modification I'd like to try is based on the epsilon-<br>> sigma form and the mixing rule is the Lorents-Bertelot's one.<br>> Could you kindly tell me the LJ potential and force routine in the epsilon-<br>> Sigma form.<br><br>There is no such code.<br><br>You can simply check for rinvsix > c6/c12.<br><br>Berk<br><br>> <br>> Thank you for advance.<br>> <br>> Makoto Yoneya, Dr.<br>> http://staff.aist.go.jp/makoto-yoneya/<br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
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