Be sure to use in Jmol
load TRAJECTORY .....
See the 11.8 documentation for that.
load TRAJECTORY "filename"
*Loads the specified file as a trajectory.*
load TRAJECTORY {first last stride} or ({i j k:l m..}) "filename"
*Loads the specified subset of models from the file as a trajectory. See load
MODELS<file:///C:/jmol-dev/workspace/Jmol-documentation/script_documentation/index.htm?ver=11.8#loadmodels>for
details. (Jmol 11.7.3)
*
load TRAJECTORY "filename" FILTER "filter specification" COORD {first last
stride} or ({i j k:l m..}) mdcrd::crdfile1
*The presence of a COORD keyword indicates that the trajectory is to be
built from a set of files that includes an AMBER molecular dynamics topology
file and associated coordinate files. FILTER is optional, but recommended.
For example, FILTER "![WAT]" prevents loading of water molecules. Any number
of coordinate files may be specified. Coordinates are loaded as a set of
trajectory steps. At least one COORD keyword must be given, and each
specification of first, last, and stride must be preceded by a COORD
keyword. {first last stride} or ({i j k:l m...}) is optional, and if not
provided defaults to {0 0 1} or ({0}), which is interpreted as "only the
first trajectory step from each file." See load
MODELS<file:///C:/jmol-dev/workspace/Jmol-documentation/script_documentation/index.htm?ver=11.8#loadmodels>for
documentation on {first last stride} and ({i j k:l m...}). (Jmol
11.7.3)
*
On Tue, Feb 10, 2009 at 8:41 AM, Kubasik, Matt
<[email protected]>wrote:
> Egon and everyone,
>
> Angel used the GROMACS utility "editconf" to convert a GROMACS file to a
> Jmol-readable file. Here's another way:
>
> Check out the trjconv utility within your installation of GROMACS:
> www.gromacs.org/documentation/reference_3.3/online/trjconv.html
>
> trjconv will read a GROMACS trajectory file (.xtc or .trr) and output a
> .pdb file, e.g.:
>
> trjconv –f trajectory.xtc –s topol.tpr –o pdbtrajectory.pdb
>
> -f = input trajectory -s = structure file (used for grompp) –o = output
> file
>
> The structure file allows trjconv to parse the trajectory.
>
> So:
> 1. use trjconv to generate a .pdb file.
> 2. load the .pdb file into Jmol Animate! ?This is the really cool part.
>
> Two more comments:
>
> Because trajectory files tend to be large, you have to be aware of the
> memory limitations of Jmol. Recently, Jmol's handling of memory errors has
> significantly improved. (Thanks, Bob!) The Jmol wiki shows how to offer
> the Jmol application more memory:
> http://wiki.jmol.org:81/index.php/Jmol_Application
>
> Note, of course, that trjconv is a trajectory editor. Options include
> skipping frames, ignoring solvent, ignoring dull parts of an otherwise
> interesting molecule, centering a molecule of interest, etc. In principle,
> these kinds of things could be duplicated in a Jmol command...but you'd be
> duplicating the trjconv utility at the expense of having Jmol work with some
> very large files.
>
> In principle, it may be possible to set up a GROMACS simulation to save a
> .pdb trajectory with only the parts of the trajectory that you want to feed
> to Jmol, but the compromise between a true analysis of a trajectory vs a
> visualization of a trajectory may be too great. And the trjconv editor
> works great.
>
> Matt
>
>
>
> -----Original Message-----
> From: Angel Herraez [mailto:[email protected]]
> Sent: Tue 2/10/2009 8:34 AM
> To: [email protected]
> Subject: Re: [Jmol-users] Jmol and GROMACS?
>
> Egon, this page of mine
> http://biomodel.uah.es/en/water/p3.htm
> was built from Gromacs data of a molecular dynamics simulation.
> Since Jmol did not read the gro file, I converted the data to pdb
> format (see details at the bottom of the page).
>
> We discussed about providing Jmol support for gro files, but I think
> it was not done -- if I remember correctly, Bob needed good sample
> files for proteins, which I don't have. See the discussion at
> http://sourceforge.net/tracker/?func=detail&atid=379136&aid=1876675&gr
> oup_id=23629<http://sourceforge.net/tracker/?func=detail&atid=379136&aid=1876675&gr%0Aoup_id=23629>
>
>
>
>
>
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--
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Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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