Gromacs 4.5 can be linked to VMD libraries so that it can
read any trajectory format that VMD can read, so now there is no file
conversion necessary. The only thing you have to do is set the VMD_PLUGIN_PATH environmental variable to point to VMD, for example I added this to my .bashrc file:
export VMD_PLUGIN_PATH=/home/apps/lib/vmd-1.9/plugins/LINUXAMD64/molfile/ It works well for DCD files. Netcdf files
are a little tricky it seems, as the plugin goes based on the file
extension. To get it to work with Gromacs you can't use the .nc
extension that VMD uses (no idea why), instead it needs to be .netcdf
You can either rename the trajectory file or just create a symbolic
link with the correct file extension. ======================= For the majority of the analisys implemented in gromacs, you don't need the tpr, a pdb and the xtc are ok. If you use the latest gromacs version (4.5.1) you need only the pdb because gromacs is able to read each format vmd is able to read. To enable this feature, you have: Now you should be able to run, for example:
If your trajectory is composed by moltiple files, you must concatenate
them using:
there is one additional issue that can arise: some of the gromacs tools
require
information about particle charges and masses, which are taken from a .tpr
file.
http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/ that can help with it. you can load your .psf and .pdb file into VMD and then do: topo writegmxtop myfile.top and it should generate a "fake" .top file that provides enough information to be able to generate a .tpr file. it will not be sufficient for simulations, but should cover the needs of the analysis tools that require a .tpr file. http://www.mail-archive.com/gmx-users@gromacs.org/msg33964.html |
Wiki >