Hi, I've been trying to turn off the electrostatic interaction between two groups (an ion-group and protein) by following the tutorial on custom table generation, but have seemed to have hit a road block.
Looking at the structure of the sample 6-12 table provided in the topology directory, I constructed my table.xvg for interactions between the two groups to be the following: #r coulomb coulomb-force 1/r^6 6/ r^7 1/12 12/r^13 0 0 0 0 0 0 0 . 0.04 0 0 -2.4414062500e+08 -3.6621093750e+10 5.9604644775e+16 1.7881393433e+19 and so on. Noting that the second and third columns are defined as zero for all steps, while the columns related to LJ are left unchanged. While for the protein-protein or ion-group ion-group interactions I provide just the standard 6-12 table. The problem comes that when I run using my modified table, the system will run but gradually explodes. I note that when I look back at my output from grompp I find a warning concerning eplison and sigma being used instead of C6 and C12, but if I swap my custom table for the sample 6-12 table (keeping the first two columns not zero) the system doesn't explode and has dynamics similar to previous simulations making use the built-in table generation. Any ideas on where I am going wrong? Here are the other specs for the simulations: Gromacs 4.0.5, OPLS/AA, berendsen pressure/temperature coupling: tau_p =0.5, tau_t=0.1, simulation temperature 283. Any help is much appreciated! -Smitty -- View this message in context: http://gromacs.5086.n6.nabble.com/Turning-off-electrostatics-between-groups-using-custom-tables-tp5000723.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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/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
