[gmx-users] Re: Gromacs issue

[Mark Abraham]

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)
>