Converting MD trajectories from NWChem to anything VMD can read.
Clicked A Few Times
2:53:04 PM PDT - Tue, May 10th 2011
Anyone knows of any way to convert from a NWChem trajectory file to anything VMD can read, for example Amber, Gromacs or NAMD trajectory format?

Thank you.

Diego

Forum Vet
2:00:31 PM PDT - Wed, May 11th 2011
Hi Diego,

What dynamics module are you running. The Car-Parrinello ab initio MD generates a xyz based motion file that can be read by VMD. For classical MD you can convert the trj trajectory file into the same format, see http://nwchemgit.github.io/index.php/Analysis#Trajectory_format_conversion for details.

Bert


UOTE=Diegoarmino May 10th 9:53 pm]Anyone knows of any way to convert from a NWChem trajectory file to anything VMD can read, for example Amber, Gromacs or NAMD trajectory format?

Thank you.

Diego

  • Guest -
8:08:27 AM PST - Wed, Dec 21st 2011
trajectory format issue
Hi to all,
I've not understood how to convert my .trj file (output of a MD run) into a more easily handled format like .pdb or .xyz.
I've the link reported above, however the following error is reported:



Last System Error Message from Task 0:: No such file or directory
 0: ARMCI aborting 0 (0).
system error message: Illegal seek





No trajectory is written (just a junk fort.69 file). What could I do to obtain my pdb/xyz file?

Thank you in advance.

Francesco

  • Guest -
9:51:46 AM PST - Fri, Dec 30th 2011
The analysis module can convert NWChem trj files into Amber crd, Discover arc or Charmm dcd files. See the 'copy' directive in the trajectory file conversion section. Individual frames out of a trajectory can be converted into pdb or xyz format using the 'write' directive.

Gets Around
5:17:13 PM PDT - Wed, Apr 29th 2015
Quote: Dec 30th 4:51 pm
The analysis module can convert NWChem trj files into Amber crd, Discover arc or Charmm dcd files. See the 'copy' directive in the trajectory file conversion section. Individual frames out of a trajectory can be converted into pdb or xyz format using the 'write' directive.


Yeah, I tried that and it is broken.

Error is: "Unresolved atom types in fragment w5" when I run a simulation with 5 H2Os in it.


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