[lammps-users] GUI lammpsfe

LAMMPS LAMMPS Mailing List Mirror
1

Does any body can help me from where I can download the GUI lammpsfe.

Regards
Rajan

2

Hi Rajan

Interesting. It looks like the company has let their web site (https://www.scifes.com) lapse. It grieves me a little bit to see this, because it’s hard to turn a profit. I know other people who have made fantastic and useful tools for LAMMPS. Maintaining software like this is a labor of love. By all means try and contact the company. But I would be ready I would move on and try looking at programs listed on this web page: https//lammps.sandia.gov/prepost.html

If you are trying to simulate molecules which use force fields which are not included with these tools, it may be possible to use other molecule builder tools (eg. mbuild, foyer, Amber tools, psfgen…?) and convert the files generated by those programs into LAMMPS format (using OpenBabel, for example).

The prepost.html we page does not include all of the useful software out there for preparing LAMMPS simulations. If you find other useful tools or services which are not listed at https://lammps.sandia.gov/prepost.html then feel free to post them.

Andrew

(OVITO, EMC, MaterialsDesign, topotools, MaterialX LTD, ATB, …)

3

I was looking for gui because most of the time will go in writing the input file for lammps which can be used in analysis of results.
But I am unable to find a good and free gui which can do this work.

4

I was looking for gui because most of the time will go in writing the input file for lammps which can be used in analysis of results.
But I am unable to find a good and free gui which can do this work.

I don’t know if this recommendation applies to you, but even if you find a good GUI tool for running molecular dynamics simulations, being comfortable with a terminal (preferably with BASH, TCSH, ZSH…) and a simple text-editor (such as jove, nano, gedit, VIM, EMACS, Atom, Sublime, VScode, or Apple TextEdit) is very useful in general. If you don’t know how to use a text editor, you will be handicapped because so many files used in science are ASCII/UTF format.)

That said, I just remembered that VIPSTER is a useful molecule drawing program with a GUI which can be used to export LAMMPS data files. (You can even add text labels, such as atom type names which will appear in the data file.) The author Sebastian even added the ability to export directly to MOLTEMPLATE format, which might be useful for people who like using that particular software. (You can draw molecules in VIPSTER and assemble them together into a simulation using moltemplate. Unfortunately, I don’t know if that particular feature works well. This conversation reminds me to test that feature. Even if it doesn’t work, you can use VIPSTER to create a LAMMPS data file for each type of molecule, and then convert it into moltemplate format. Here’s a long and somewhat confusing example of this procedure here. If I have time, I might try this again to see if these instructions need to be updated. The main problem with moltemplate is that you must select the correct atom type names for every type of atom in your molecule. Programs like EMC will attempt to do this for you. EMC is very useful. See below. You also need to find a way to generate the partial charges for each atom. Depending on the force field you are using EMC and Moltemplate can do this. LAMMPS also has some features for automatic charge assignment.)

I should warn you that when I tried using VIPSTER 2 years ago, I noticed that atoms do not move the way you expect when you click on them. However, perhaps that issue has been fixed in more recent versions. I think that even with these limitations, VIPSTER is a very useful tool. It really gives you maximal control over how to build your simulation exactly the way you want it.

I am a biased source of information. For what it’s worth, here are some other recommendations to consider:

  1. The EMC program can prepare simulation files for LAMMPS and it can determine atom type and force field information from the name of the element in the SMILES string you provided. Simulations built with EMC tend to have the molecules placed randomly. If you want more control over the positions of the molecules you can prepare tiny simulations containing only one molecule, and use MOLTEMPLATE+ltemplify.py or VMD+topotools (or LAMMPS for periodic structures) to make copies of these molecules and place them exactly where you want them.

  2. ATB molecule repository is a fantastic resource, especially for small organic molecules. Molecules from ATB include atom type, accurate force field, and charge information, and you can assemble them together into a simulation box using moltemplate…

  3. Topotools is also a very, very useful tool. I use it all the time.

Please feel free (anyone reading this) to add any programs I left out.

Creating simulation input files for LAMMPS (or any MD program) is a skill that takes time to learn. I hope this helps get you started.

Andrew