Please keep GROMACS correspondence on the mailing list. You stand a much
better chance of getting a useful reply that can be saved for the future.
On 19/04/2010 10:35 PM, Martin Vartorelli wrote:
Hi, I'm a Gromacs user. I have a problem and I couldn't find any
answer in the mailing list and I'm very hurry.
That's irrelevant to whether you should be pestering an individual who
hasn't solicited your correspondence :-)
I'm asking you because I think that you already has an issue like mine.
No, I've never had an issue like yours. You don't want to irritate the
people who might be best place to help you by spamming them.
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?
Make sure you've read the manual and relevant wiki web page thoroughly,
and you should experiment on a simple system first.
Mark
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'?
Any help will be appreciated.
Thank you.
Lic. Martin R. Vartorelli
INTEC-UNL-CONICET
(Institute of Technological Development for the Chemical Industry)
Güemes 3450
3000 Santa Fe, Argentina
Phone: +54 (342) 455-9174 (ext. 2072, office PPB23)
--
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
