#135 GROMACS gro input

closed
nobody
5
2009-07-14
2008-01-21
No

I would like to have Jmol read GROMACS output file format, .gro

Informal description:
(http://en.wikipedia.org/wiki/Chemical_file_format#GROMACS_format)
The GROMACS file format family was created for use with the molecular simulation software package GROMACS. It closely resembles the PDB format but was designed for storing output from molecular dynamics simulations, so it allows for additional numerical precision and optionally retains information about particle velocity as well as position at a given point in the simulation trajectory. It does not allow for the storage of connectivity information, which in GROMACS is obtained from separate molecule and system topology files. The typical file extension for a GROMACS file is .gro.

Official description:
http://www.gromacs.org/documentation/reference/online/gro.html

I am attaching some example files taken from the examplees in GROMACS installation (a peptide, a box of water molecules, a box of urea in water) and, for reference, the equivalent pdb files obtained using the Gromacs converter program, "editconf".

Discussion

  • Angel Herraez

    Angel Herraez - 2008-01-21

    example gro files

     
    Attachments
  • Nicolas

    Nicolas - 2008-01-21

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    I would also be interested in Jmol being able to read such files.

    GROMACS is one of the molecular dynamic simulations program used by Folding@Home.
    That would be a nice enhancement for http://www.jmol.org/fah , especially if the simulation trajectory can be retrieved as a multiframe model.

     
  • Bob Hanson

    Bob Hanson - 2008-02-02

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    Shouldn't be a problem. May I implement the trajectory as a vibration vector?

    Q: What is the following all about:

    box vectors (free format, space separated reals), values: v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y), the last 6 values may be omitted (they will be set to zero). Gromacs only supports boxes with v1(y)=v1(z)=v2(z)=0.

    Q: How should Jmol infer an atom type (chemical element) from the above information? Please supply some examples with two-character element symbols such as Fe, Li, or Cl.

    Q: Is there something that Jmol could use to identify this as a protein? If so, then we could create helices and such.

    Q: Please provide a protein example that involves multiple chains.

    Q: Please provide a protein example that involves a trajectory.

     
  • Nobody/Anonymous

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    I'm waiting for response to my questions in order to move forward with this.

    Bob Hanson

     
  • Angel Herraez

    Angel Herraez - 2008-02-15

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    Sorry, I have no trustable files in this format and I don't work with it, so cannot provide sensible suggestions. What I was using is a box full of water molecules.
    Nico should have proteins.

    I tried some example gro files by converting them to pdb. The atom IDs seem to be identical in both.

    As far as I have understood, there seems to be no support for chain IDs in gro format.

     
  • Nicolas

    Nicolas - 2008-10-15

    I have uploaded an example of files produced by the Gromacs core used by Folding At Home :
    http://test04145.mutu.sivit.org/p2492.zip

    Do you think something can be read by Jmol among all the files ?

    Zip contents :
    * current.xyz, current.xyz_tmp : folding at home xyz files (currently read by Jmol)
    * wudata_01.bed : contents ? binary format
    * wudata_01.bxv : contents ? text format
    * wudata_01.chk : contents ? binary format
    * wudata_01.dat : contents ? binary format
    * wudata_01.eng : contents ? text format
    * wudata_01.log : log. text format. http://www.gromacs.org/documentation/reference/online/log.html
    * wudata_01.xtc : trajectory. binary format (xdr). http://www.gromacs.org/documentation/reference/online/xtc.html
    * wudata_01.xyz : contents ? binary format
    * wudata_01CP.arc : contents ? binary format
    * wuinfo_01.dat : contents ? binary format

     
  • Bob Hanson

    Bob Hanson - 2009-07-08

    GROMACS reader added to Jmol 11.7.47. Coordinates assumed in nanometers; read as PDB file, with secondary structure assigned automatically and elements inferred from atom names. UREA and SOL included in "solvent" set.

     
  • Bob Hanson

    Bob Hanson - 2009-07-08

    also, force vectors included as vibrations.

     
  • Angel Herraez

    Angel Herraez - 2009-07-14
    • status: open --> closed
     

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