[gmx-users] gromacs 4.5.4 analysis tools

Roland Schulz roland at utk.edu
Sun Apr 3 22:47:41 CEST 2011


depends on the tool. If the tool just need the coordinates or just
velocities (dcd/vel) you don't need to convert anything because the tools
can use the VMD plugins to read dcd. If the tool needs a tpr file (e.g.
carges) than you need to create one. In most cases the easiest solution to
do this is to use pdb2gmx. If you have a non-standard molecule for which no
rtp exists you could also use psfgen+top (http://www.benlabs.net/psfgen+top/
If the tool needs coordinates and velocities, let me know and I'll think of


On Sun, Apr 3, 2011 at 3:06 PM, Molecular Dynamics <
moleculardynamics at yahoo.com> wrote:

> Dear gmx users,
> I’m a NAMD user and want to use gromacs 4.5.4 analysis tools for my NAMD
> output files. I have some NAMD output files : output.coor , output.vel ,
> output.dcd (binary coordinate trajectory output file). Can I convert these
> output files into gromacs output files and use gromacs 4.5.4 analysis
> tools ? If it’s possible to do it, could you please explain this job ?
> Thanks in advanceM
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