[gmx-users] Modifying Lennard-Jones cross term

lloyd riggs lloyd.riggs at gmx.ch
Wed Jul 4 15:33:45 CEST 2012


Ill give that a shot from memory of a discussion some time ago, which you could probably track down on the e-mails of past search engine.  I think it has to do with force field types, either they list the sigma values, or direct 6, 12 or derived LJ parameters,  so it would be related to which force field you use.

Otherwise they are in the .rtp, .itp files for specific force fields as tables, and I assume as such you could then put anything you wished in there real or not, as the software would just take the table value.

Although I assume someone else has more direct advice, personally though I dont think there would be much of a difference of it unless your atoms pairs have different sigma values than those used in gromacs.  You might, if you wished only 2 atoms, have to define an entry for those explicitly, giving some names different from the other things in the .rtp, .itp files, then the respective sigmas in the parameters.  The bulletin/email list also has ample things on this (modification of the files) as well, but the files are all strait forward if you just look at them in an editor.  Defining the resultant, (example sigma_12) might be hard however, as in either case it still plugs in the parameter to an equation.

Otherwise you could plot distances and do the lj calculation by hand, but it might get heck-tick if you include any solvent, or other effects...

Good luck

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Wed, 4 Jul 2012 17:45:56 +0900 (KST)
> Von: Hyungjun Kim <hyungjun96 at kaist.ac.kr>
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] Modifying Lennard-Jones cross term

>    Dear GMX users,
>    This is Hyungjun Kim.
>    I try to modify the len?ard jones parameter explicitly.
>    I knew that gromacs provide the com?ination rule such as
>    sigma_12=(sigma_1 + sigma_2 ) /2 like.
>    I fin? that some specific interaction is quite important, so I want to
>    give expl?cit sigma_12 value for some combination.
>    Could you give me any advi?e?
>    Thank you in advance.
>    Regards,
>    김형??D8 드림
>    ---
>    Hyungjun Kim,
>    Quantum and Computation?l Chemistry Laboratory,
>    Department of Chemistry, KAIST,
>    Daejeon 305?701, Korea
>    e-mail: [1]hyungjun96?kaist.ac.kr or [2]jun0906 at kai?t.ac.kr
>    phone : 042-350-2861
>    mobile phone : 010-8537-5051
>    web : http://qclab.kaist.ac.kr
> References
>    Visible links
>    1. file:///tmp/3D"mailto:hyungjun96 at kaist.ac.kr"
>    2. file:///tmp/3D"mailto:jun0906 at kaist.ac.kr"
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