Re: gromacs analysis tools

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Apr 03 2011 - 14:28:04 CDT

all,

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.

the VMD topotools plugin has an (currently undocumented) feature
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.

cheers,
    axel.

On Sun, Apr 3, 2011 at 2:47 PM, Francesco Oteri
<francesco.oteri_at_gmail.com>wrote:

> 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
>
>
>
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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