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Hi,<br><br>I don't want to get into discussions on drugs and I don't know if you<br>already switched package, but I'l post my answer anyhow.<br><br>The energy groups in each pair on your energygrp_table line should<br>be separated by a space.<br><br>The table files should contain all columns, unused columns are allowed<br>to contain zero's, since they are simply ignored.<br><br>PS:<br>Please don't mail me directly with questions on Gromacs,<br>apart from the good reasons already given on the list,<br>this is a strong incentive for me not to answer your mail.<br><br>Berk<br><br>> From: mrvartorelli@gmail.com<br>> Date: Mon, 19 Apr 2010 10:05:59 -0300<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Problem with tabulated potentials for 3 different atoms<br>> <br>> I'm trying to use tabulated potentials for a very simple system: a<br>> polymer chain with only 3 kind of atoms: A, B and C, all of it with<br>> zero charge.<br>> <br>> A--(B)n--C<br>> <br>> The only interactions that accounts are AB, AC, BB and CC, so in my<br>> mdp file I have writen:<br>> <br>> coulombtype = user<br>> vdw-type = user<br>> energygrps = A B C<br>> energygrp_table = AB AC BB BC<br>> <br>> Also, I'm using tabulated bonded potentials for bonds and angles.<br>> <br>> The main questions are how to tell to mdrun that he must read my table<br>> files and can I be sure that the reading is OK?<br>> <br>> For the bonding part I have the following table files:<br>> <br>> table_b1.xvg<br>> table_a1.xvg<br>> table_a2.xvg<br>> table_a3.xvg<br>> <br>> And in the mdrun commandline I'm using the option -tableb table.<br>> But how to handle the non bonding table files?<br>> <br>> table_A_B.xvg<br>> table_A_C.xvg<br>> table_B_B.xvg<br>> table_B_C.xvg<br>> <br>> Must I write<br>> <br>> energygrps = A B C<br>> energygrp_table = AC BB BC<br>> <br>> in the mdp file and use the tables<br>> <br>> table.xvg<br>> table_A_C.xvg<br>> table_B_B.xvg<br>> table_B_C.xvg<br>> <br>> with the command line for mdrun saying -table table.xvg?<br>> <br>> Another thing, because the tables doesn't have to contain only zero columns...<br>> Can I put anything on the f and f' columns (because the charge of my<br>> atoms is zero)?<br>> Can I put (for example) 0.5 in the g and g' columns and my potential<br>> (and the force) minus 0.5 in columns h and h'?<br>> <br>> I'm using the 4.0.7 version.<br>> <br>> Again as an abstract:<br>> <br>> System: 1 chain A--(B)n--C<br>> Bonds: A-B = B-B = B-C --> only one table: table_b1.xvg<br>> Angles: A-B-B, B-B-B, B-B-C --> 3 tables: table_a1.xvg, table_a2.xvg,<br>> table_a3.xvg<br>> Charges: none<br>> VDW interactions: A-B, A-C, B-B, B-C --> 4 tables table_A_B.xvg,<br>> table_A_C.xvg, table_B_B.xvg, table_B_C.xvg<br>> <br>> *.mdp lines:<br>> coulombtype = user<br>> vdw-type = user<br>> energygrps = A B C<br>> energygrp_table = ?<br>> <br>> run commandline:<br>> mdrun -s -c -e -x -g -table ? -tableb ?<br>> <br>> Any help will be appreciated.<br>> <br>> Thank you.<br>> <br>> Martin R. Vartorelli<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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