I'm trying to use tabulated potentials for a very simple system: a polymer chain with only 3 kind of atoms: A, B and C, all of it with zero charge.
A--(B)n--C The only interactions that accounts are AB, AC, BB and CC, so in my mdp file I have writen: coulombtype = user vdw-type = user energygrps = A B C energygrp_table = AB AC BB BC Also, I'm using tabulated bonded potentials for bonds and angles. The main questions are how to tell to mdrun that he must read my table files and can I be sure that the reading is OK? For the bonding part I have the following table files: table_b1.xvg table_a1.xvg table_a2.xvg table_a3.xvg And in the mdrun commandline I'm using the option -tableb table. But how to handle the non bonding table files? table_A_B.xvg table_A_C.xvg table_B_B.xvg table_B_C.xvg Must I write energygrps = A B C energygrp_table = AC BB BC in the mdp file and use the tables table.xvg table_A_C.xvg table_B_B.xvg table_B_C.xvg with the command line for mdrun saying -table table.xvg? Another thing, because the tables doesn't have to contain only zero columns... Can I put anything on the f and f' columns (because the charge of my atoms is zero)? Can I put (for example) 0.5 in the g and g' columns and my potential (and the force) minus 0.5 in columns h and h'? I'm using the 4.0.7 version. Again as an abstract: System: 1 chain A--(B)n--C Bonds: A-B = B-B = B-C --> only one table: table_b1.xvg Angles: A-B-B, B-B-B, B-B-C --> 3 tables: table_a1.xvg, table_a2.xvg, table_a3.xvg Charges: none VDW interactions: A-B, A-C, B-B, B-C --> 4 tables table_A_B.xvg, table_A_C.xvg, table_B_B.xvg, table_B_C.xvg *.mdp lines: coulombtype = user vdw-type = user energygrps = A B C energygrp_table = ? run commandline: mdrun -s -c -e -x -g -table ? -tableb ? Any help will be appreciated. Thank you. Martin R. Vartorelli -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
