[gmx-users] truncated LJ potential

Berk Hess gmx3 at hotmail.com
Mon Jan 10 17:25:17 CET 2011

> From: makoto-yoneya at aist.go.jp
> To: gmx-users at gromacs.org
> Date: Mon, 10 Jan 2011 23:57:46 +0900
> Subject: [gmx-users] truncated LJ potential
> Dear David and Hess:
> Thanks a lot for quick replies.
> >> please look into gromacs' table potential functionality, it is described 
> >> in the manual, and you won't have to program anything
> >> UNLESS the sigma is different for different atom pairs, in that case I'm 
> >> not sure if it will work.
> The target system has many different atom types with different sigmas (and
> epsilons).
> I'd like to switch between the standard LJ potential simulation and the
> corresponding
> repulsion only one with the same LJ parameter sets for the real compounds
> not simplified models.
> > You can make different tables for interactions between groups of atoms
> with
> > different sigma's by putting these groups in different energy groups,
> > but this might get tedious.
> As the modification which I'd like to try is very simple one from the 
> original LJ function, I'd like to try to modify the code instead of
> supplying
> many kinds of the tables for each pairs of atom types.
> > You can also set the environment variable nb_generic.c and modify
> > src/gmxlib/nonbonded/nb_generic.c, but might lead to somewhat
> > slower simulations.
> The LJ potential and force code in the above looks like in the c6-c12 form
> not in epsilon-sigma one.
> The LJ potential modification I'd like to try is based on the epsilon-
> sigma form and the mixing rule is the Lorents-Bertelot's one.
> Could you kindly tell me the LJ potential and force routine in the epsilon-
> Sigma form.

There is no such code.

You can simply check for rinvsix > c6/c12.


> Thank you for advance.
> Makoto Yoneya, Dr.
> http://staff.aist.go.jp/makoto-yoneya/
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110110/6ecf8876/attachment.html>

More information about the gromacs.org_gmx-users mailing list