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Re: [lammps-users] Export Material Studio Coarse Grain
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Re: [lammps-users] Export Material Studio Coarse Grain


From: Andrew Jewett <jewett@...1937...>
Date: Tue, 22 Aug 2017 18:00:35 -0700

Most of the molecule building tools for LAMMPS are listed at:

http://lammps.sandia.gov/prepost.html

If you are going to use coarse grained models, I suggest avoiding
software tools which limit you to a particular style of force-field or
atom_style.

Disclaimer: I wrote "moltemplate".  This software is was designed with
the intent of building coarse-grained models.  It is quite general and
it is distributed with a lot of coarse grained examples you can try
and modify.

In addition, check out "Topotools".  It uses TCL and it is well
integrated with VMD.

Both moltemplate and topotools work with nearly all atom_styles and
force-field styles (pair, bond, angle, dihedral, improper), including
hybrid styles, and they can extract coordinate data from xyz and pdb
files.  (I frequently use tools like PACKMOL to generate XYZ files
which moltemplate can read.)

You can also try creating a LAMMPS DATA file yourself manually, as
Vanessa suggested.

--- regarding Materials Studio and XYZ files ---

Force field and topology information are not stored in XYZ files, only
atom coordinates.

Personally, I agree with Vanessa.  I think of Materials Studio and
"msi2lmp" as tools for building all-atom systems.  I cannot comment
whether they would be suitable for building your own custom
coarse-grained models.  Furthermore, my impression is that msi2lmp is
not very actively developed and maintained.  People occasionally post
complaints on the mailing list about that tool.

I hope this helps.

Andrew

On Tue, Aug 22, 2017 at 2:20 PM,  <arizvi@...1290...> wrote:
> Hi,
>
>
>
> I have built a coarse grain model of clay in materials studio and assigned
> charges to it. I’d like to export it into a xyz file so that I can use it in
> lammps. Is there an easy method to accomplish this?
>
>
>
> I’ve tried using msi2lmps to see if I can get a usable file. When I try this
> tool I don’t get any outputs and I’m not sure what to look for.
>
>
>
> I am a beginner so any help would be appreciated,
>
>
>
> Thanks,
>
>
>
> Anam
>
>
>
>
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