Re: gromacs analysis tools

From: Francesco Oteri (francesco.oteri_at_gmail.com)
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
vmd_directory/plugins/LINUXAMD64/molfile).

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:
> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
>
> or in VMD using the animate command:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node119.html
>
> 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
>>
>
>

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