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Can some body please tell me whether avagadro can create lammps input data file

Arun

On Tue, Jun 24, 2014 at 8:31 PM, S Arun Srikant Sridhar
ss3763@drexel.edu wrote:

Can some body please tell me whether avagadro can create lammps input data
file

It cannot at this time - I have been looking into LAMMPS, and how we
might produce input for MD codes in general but we don’t have anything
working yet (that I am aware of at least). I did add some support for
XYZ trajectories, GROMACS files, and am hoping to add some more in the
future but this has mainly been limited to the output from MD codes.

Marcus

It cannot at this time - I have been looking into LAMMPS, and how we
might produce input for MD codes in general but we don’t have anything
working yet (that I am aware of at least).

That’s not quite right. There were some patches for Avogadro v1 to write simple LAMMPS input. The main problem has been that people have requested the feature, but not really outlined what they would want a LAMMPS generator to do. (There are just way too many LAMMPS options.)

Arun, can you explain a bit what you do with LAMMPS and what you might want an Avogadro interface to do?

Perhaps if we can identify key features that people use a lot, we can do something similar to the quantum codes.

Thanks!
-Geoff

P.S. There are a number of LAMMPS users here at Pitt and Carnegie Mellon, but no one has been able to give me more than just “oh, I’d like one please.” A few paragraphs or a sketch of what an interface would do is extremely helpful.


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

On Tue, Jun 24, 2014 at 11:22 PM, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

It cannot at this time - I have been looking into LAMMPS, and how we
might produce input for MD codes in general but we don’t have anything
working yet (that I am aware of at least).

That’s not quite right. There were some patches for Avogadro v1 to write simple LAMMPS input. The main problem has been that people have requested the feature, but not really outlined what they would want a LAMMPS generator to do. (There are just way too many LAMMPS options.)

Sorry - I missed, and thought we had ported most of the input
generators to Avogadro 2 it. It is in the quantuminput folder which is
kind of confusing :wink: I would love to look at porting it too, and
seeing what options people might like there. Thanks for pointing that
out.

Arun, can you explain a bit what you do with LAMMPS and what you might want an Avogadro interface to do?

Perhaps if we can identify key features that people use a lot, we can do something similar to the quantum codes.

That would be great to look into, I would really like to extend what
we do to some of the major MD codes.

P.S. There are a number of LAMMPS users here at Pitt and Carnegie Mellon, but no one has been able to give me more than just “oh, I’d like one please.” A few paragraphs or a sketch of what an interface would do is extremely helpful.

If I came out to Pittsburgh is there any chance of meeting with some
of them do you think? I would love to explore this further, and have
been digging into LAMMPS and GROMACS.

Thanks,

Marcus

Thank you very much for your help. I did pose the same question to lammps users list. The reply was to use to use topo tools and moltemplate. But I like the GUI of avagadro compared to other gui’s such as jmol. Coming to the problem. I am actually simulating an epoxy in lammps. I would want to generate a lammps data file for this rather having me to do the grunt work in editing the output from an xyz or pdb file from any molecular viewers.

Thanks
Arun

On 06/24/14, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

It cannot at this time - I have been looking into LAMMPS, and how we
might produce input for MD codes in general but we don’t have anything
working yet (that I am aware of at least).

That’s not quite right. There were some patches for Avogadro v1 to write simple LAMMPS input. The main problem has been that people have requested the feature, but not really outlined what they would want a LAMMPS generator to do. (There are just way too many LAMMPS options.)

Arun, can you explain a bit what you do with LAMMPS and what you might want an Avogadro interface to do?

Perhaps if we can identify key features that people use a lot, we can do something similar to the quantum codes.

Thanks!
-Geoff

P.S. There are a number of LAMMPS users here at Pitt and Carnegie Mellon, but no one has been able to give me more than just “oh, I’d like one please.” A few paragraphs or a sketch of what an interface would do is extremely helpful.


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/


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Hi,

Possibly not relevant as it’s more about analysis then input generation,
but I just thought I’d mention mdanalysis:

https://code.google.com/p/mdanalysis/

I know it’s python, but I think it’s relatively simple to access the
underlying C arrays, so might be a quick way to add initial support for
some of the trajectory formats out there?

Best wishes,

Jens

On 25 June 2014 04:28, Marcus D. Hanwell marcus.hanwell@kitware.com wrote:

On Tue, Jun 24, 2014 at 11:22 PM, Geoffrey Hutchison geoff.hutchison@gmail.com
wrote:

It cannot at this time - I have been looking into LAMMPS, and how we
might produce input for MD codes in general but we don’t have anything
working yet (that I am aware of at least).

That’s not quite right. There were some patches for Avogadro v1 to write
simple LAMMPS input. The main problem has been that people have requested
the feature, but not really outlined what they would want a LAMMPS
generator to do. (There are just way too many LAMMPS options.)

Sorry - I missed, and thought we had ported most of the input
generators to Avogadro 2 it. It is in the quantuminput folder which is
kind of confusing :wink: I would love to look at porting it too, and
seeing what options people might like there. Thanks for pointing that
out.

Arun, can you explain a bit what you do with LAMMPS and what you might
want an Avogadro interface to do?

Perhaps if we can identify key features that people use a lot, we can do
something similar to the quantum codes.

That would be great to look into, I would really like to extend what
we do to some of the major MD codes.

P.S. There are a number of LAMMPS users here at Pitt and Carnegie
Mellon, but no one has been able to give me more than just “oh, I’d like
one please.” A few paragraphs or a sketch of what an interface would do is
extremely helpful.

If I came out to Pittsburgh is there any chance of meeting with some
of them do you think? I would love to explore this further, and have
been digging into LAMMPS and GROMACS.

Thanks,

Marcus


Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft


Avogadro-Discuss mailing list
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Dear everyone,

I would like to know what is the current status of this issue.
Specifically, I have some .sdf files from Pubchem and would like to use avogadro to translate the geometry into a lammps geometry input.
I have followed this tutorial: LAMMPS input for water - Avogadro
but it only partially solves the problem since I can obtain neither “coords”, nor “types”, “charges” and so on…
Is there any available tool that I can use?

Thank you
Marco

I have found this, but not sure if it can translate xyz to lammps geometry file.

BR
Marco

A collaborator (who uses LAMMPS extensively) suggested http://moltemplate.org

They sent a script which would help Avogadro2 write MolTemplate files.

The LAMMPS builder in Avogadro2 has been extensively reworked. But since I don’t use LAMMPS, I can’t say if it meets your needs: