molecular design (?)

LAMMPS LAMMPS Mailing List Mirror
1

Hello,

This question is not related to LAMMPS. But many may be know this.

Is there a good free software for molecular design. I mean I have a diagram of an organic molecule and I would like to create an xyz format coordinate file for the molecule (perhaps using molecular mechanics). I would like something in Linux (preferably Ubuntu environment). But would also like to know a good software to do this on windows.

Thanks,

Vivek

2

Here's a few:

1) avogadro.openmolecules.net

2) VMD/molfacture (free for academics)
http://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/

3) PACKMOL
http://www.ime.unicamp.br/~martinez/packmol/
http://www.ime.unicamp.br/~martinez/packmol/examples/index.html

I have not tried the next two programs, but they look okay:

4) MMTK
http://dirac.cnrs-orleans.fr/MMTK/

5) Molecular Dynamics Studio:
http://sourceforge.net/projects/moleculardynami/

I'm sure there are other worthy software programs I am not aware of.
Hopefully other people will post whatever I omitted.

Cheers!

Andrew

For a discussion of software used specifically or building LAMMPS data
files, check out this thread:
http://sourceforge.net/mailarchive/message.php?msg_id=30418794

3

I probably should not have posted that. Many of the entries on that
list I posted probably aren't very helpful for small organic
molecules. Perhaps the following list has one or two other useful
links.. (I have a friend who like yasara at one point.) Cheers.

http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling

4

As always I have to plug project aten here. (projectaten.org) It allows you to write a custom force field and then minimize the molecule with respect to it. It can find bonds, angles, and dihedrals based on the forcefield and defined bonds. It outputs to xyz and a number of other formats, but it does not play directly with lammps. The last system I built for lammps I used a combination of aten and moltemplate to set up. Aten was used to identify the angles and bonds. The information was reprocessed hackishly in excel to feed it to moltemplate. It worked like a charm.

Salo

5

I see that packmol website is not working for the last 4 days. Does anybody has a source file that they can share with me ?

Thanks,

Vivek

6

Never used it thus no idea which is the last version but there are a
bunch posted in the link below.

http://code.google.com/p/packmol/downloads/list

Don't be shy to browse the web before requesting help. Its free (not
the connection though), very informative (or viceversa :wink: and fun so,
why not go surfing at your own risk when looking for things?...
Carlos

7

I emailed Leandro to let him know the packmol web site is down.
Hopefully he will get it back up soon. It has a few nice examples and
pictures (and a manual).
Thanks for the heads up.

Andrew