Feature Requests item #1876675, was opened at 2008-01-21 19:49 Message generated for change (Settings changed) made by aherraez You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1876675&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: New IO Format Group: None >Status: Closed Priority: 5 Private: No Submitted By: Angel Herraez (aherraez) Assigned to: Nobody/Anonymous (nobody) Summary: GROMACS gro input Initial Comment: 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". ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-07-08 19:15 Message: also, force vectors included as vibrations. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-07-08 19:15 Message: 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. ---------------------------------------------------------------------- Comment By: Nicolas (nicove) Date: 2008-10-15 20:38 Message: 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 ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2008-02-15 14:32 Message: Logged In: YES user_id=1065324 Originator: YES 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. ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2008-02-15 13:55 Message: Logged In: NO I'm waiting for response to my questions in order to move forward with this. Bob Hanson ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2008-02-02 06:11 Message: Logged In: YES user_id=1082841 Originator: NO 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. ---------------------------------------------------------------------- Comment By: Nicolas (nicove) Date: 2008-01-21 21:25 Message: Logged In: YES user_id=1096197 Originator: NO I would also be interested in Jmol being able to read such files. GROMACS is one of the molecular dynamic simulations program used by fold...@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. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1876675&group_id=23629 ------------------------------------------------------------------------------ Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
