> 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,
>>Ignoring warnings is a great way to waste time, and if you can't provide >>specific details of what it was, you're unlikely to get specific help. The warning is as follows: WARNING 1 [file pep_ion.top, line 1218]: Using sigma/epsilon based combination rules with user supplied potential function may produce unwanted results. I've looked into this on the mailing list, but it appears that so long as the forces are what I expect them to using the standard tables, I should be able to ignore this warning. Hopefully I have not misread the previous threads. > 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? >>Can't tell. What's the "ion group"? Does it even get close to Protein? The "ion group" is a set of 50 dissociated ions (25 K+, 25 Cl-). The ions under standard simulation conditions (non-custom interaction table) rarely have K+ or Cl- atoms coming within 0.5 angstroms of any atom of the protein group; but they do still happen. If it helps my .mdp file for the simulation is attached. http://gromacs.5086.n6.nabble.com/file/n5000727/md.mdp md.mdp Thanks again, hope this clears up my question. -Smitty -- View this message in context: http://gromacs.5086.n6.nabble.com/Turning-off-electrostatics-between-groups-using-custom-tables-tp5000723p5000727.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
