2 sep 2012 kl. 20.47 skrev Smitty: > > >> 1) That .mdp applies different tables to K-K, protein-protein and all >> other interactions, which isn't what you've said you've done. >> 3) Your life will be simpler if you use energygrp_table only for the >> group-group interactions you want to change, and leave the default >> interactions normal. It will also be faster, because using tabulated >> interactions is much slower than the normal ones. >> >> Mark >> -- >> gmx-users mailing list gmx-users@ >> 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-request@. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > Thanks mark, I have since gone back and modified the .mdp file after > re-reading the tutorial and manual and have come up with the new attached > .mdp file ( http://gromacs.5086.n6.nabble.com/file/n5000746/md.mdp md.mdp , > which I think removes the problems you highlighted in 1) and 3). > > I no longer have an exploding system; however, when I run g_energy on the > output .edr file from a short run (looking at the K+ and protein energy > groups) I get the following output: > > Energy Average RMSD Fluct. Drift > Tot-Drift > ------------------------------------------------------------------------------- > Coul-SR:K+-K+ 551.07 208.162 89.6287 0.69831 > 650.828 > LJ-SR:K+-K+ 1.43168 0.794798 0.668453 0.00159813 > 1.48946 > Coul-14:K+-K+ 0 0 0 0 > 0 > LJ-14:K+-K+ 0 0 0 0 > 0 > Coul-SR:K+-Protein -6994.99 1978.5 1003.44 -6.33779 > -5906.85 > LJ-SR:K+-Protein 52.3447 13.7398 11.2697 0.0292135 > 27.2271 > Coul-14:K+-Protein 0 0 0 0 > 0 > LJ-14:K+-Protein 0 0 0 0 > 0 > Coul-SR:Protein-Protein -246.639 43.9503 30.246 0.11852 > 110.461 > LJ-SR:Protein-Protein -81.9209 10.2086 9.29929 0.0156543 > 14.5899 > Coul-14:Protein-Protein 1477.91 19.7693 16.2154 -0.0420325 > -39.1745 > LJ-14:Protein-Protein 158.219 11.1455 10.5729 -0.0131077 > -12.2164 > > Which is closer to what I am going for, but I would expect that the > Coul-14/LJ-14 K+-K+ would not be zero. Any ideas on what I am still not > doing correct? Thanks for all the help. >
Why would you have 1-4 interactions for monoatomic species? Or between different molecules for that matter? > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Turning-off-electrostatics-between-groups-using-custom-tables-tp5000723p5000746.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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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
