Re: gromacs analysis tools

From: Francesco Oteri (
Date: Sun Apr 03 2011 - 13:47:19 CDT

Dear M,
dcd files are readable by GROMACS. To use these feature, you have to
install VMD.
Once VMD is installed, the environment variable VMD_PLUGIN_PATH should
point to the VMD directory containing library for file reading (usually

Now you should be able to run, for example:
g_rms -f .dcd -s .pdb

If your trajectory is composed by moltiple files, you must concatenate
them using:
trjcat -f *.dcd *.dcd *.dcd -o trajectory.xtc

Usually, the timeof the different frames is 0 so you should change the
time for each frame running trjconv on trajectory.xtc

Il 03/04/2011 17:45, Joshua Adelman ha scritto:
> Two possible ways to do this are using catdcd:
> or in VMD using the animate command:
> Best of luck,
> Josh
> On Apr 3, 2011, at 5:54 AM, Molecular Dynamics wrote:
>> Dear namd users,
>> Iím a new 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 itís possible to do it, could you
>> please explain this job ?
>> Thanks in advanceM

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:04 CST