[gmx-users] Tabulated potentials
Hi Gromacs users, previously I've posted my situation with a simulation and I'm still confused: I have 3 groups of different atoms: A, B and C, and tabulated bonding and non-bonding potentials. The tabulated bonded potentials are specified in the files: table_b1.xvg table_a1.xvg table_a2.xvg table_a3.xvg Because the systems is simply this molecule: A--(B)n--C, the *.mdp file contains the following: coulombtype = user vdw-type= user energygrps = A B C energygrp_table = A B A C B B B C >From the manual and tutorials I understand that, for the non bonding part of U, I can suply a file called "table.xvg" that contains the 7 non-zero columns for r, f, f', g, g', h and h'. The file "table.xvg" must contain the functions for AB interactions and the remaining interactions must be in the files "table_A_C.xvg", "table_B_B.xvg" and "table_B_C.xvg". So, in the command line I can write: mdrun -table table.xvg -tableb table I'm right? As a test I have also included the file "table_A_B.xvg" (the same potential functions that "table.xvg") in the same directory, and when I look at the log file it shows that this file is readed too. I'm still unclear... how must I specify the files in an univocal way for the non bonding interactions that I want? Gromacs version: 4.0.7 Any help will be appreciated. Martin. PD: I've received some private e-mails explaining to me some issues about spam, mailing lists, private mails, etc. Thanks to all and I apologize if I've bother someone, it wasn't my intention. And for those who spontaneously shows me their support, I don't want it and I don't need it! -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with tabulated potentials for 3 different atoms
Berk: Thanks for the help, and thanks too to the other members of the list who helped me. My simulation is working now with some energy problems, but this is another problem not related to the software. The missing space characters were a typing mistake. About drugs and other subjets of your post, they are all out of my research interests. Maybe you wanted to say these to another user? Martin. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with tabulated potentials for 3 different atoms
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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
