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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 18:41:55 -0700

On Tue, Aug 22, 2017 at 5:06 PM, Vanessa Oklejas <voklejas@...24...> wrote:
> See http://lammps.sandia.gov/doc/99/data_format.html for the details
> on how LAMMPS reads in structures

This is also a good suggestion, regardless.  It's a good idea to read
about the format for LAMMPS data files regardless how you generate
them.  You can store atom coordinates, bond topology, and even force
field parameters inside these files.  And that's a good link because
it really demonstrates the file format.  More comprehensive (but
somewhat harder to read) documentation is available at:

http://lammps.sandia.gov/doc/read_data.html
http://lammps.sandia.gov/doc/atom_style.html

Cheers (and thanks)

Andrew

(More details:  Axel and I generally prefer storing force-field
parameters in a separate input script file containing pair_coeff,
bond_coeff, angle_coeff, ... commands.  For a good example of that
file format, see:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2/in.step2e-2.
Both topotools and moltemplate can generate these commands.
Moltemplate stores them in a file named "system.in.settings".)

On Tue, Aug 22, 2017 at 6:11 PM, Vanessa Oklejas <voklejas@...24...> wrote:
> I'd 2nd the use of moltemplate for building coarse-grained models as I've
> used it myself and I found it worked well.
> On Aug 22, 2017 6:01 PM, "Andrew Jewett" <jewett@...1937...> wrote:
>>
>> 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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>>
>>
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