normal Use of TNG to visualize a Martini trajectory

  • alfredo
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4 years 11 months ago #8087 by alfredo
Hi,
I am new user to martini. I would like to visualize a Martini trajectory. There has been suggestions in recent posts to use tng format and to visualize this file with VMD. I converted the xtc trajectory to tng but the normal binaries provided by the VMD website don't read that file format. I wonder if some of you could describe the steps needed to compile the necessary VMD plugin to read this file format.
Thanks,

Alfredo

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4 years 11 months ago #8089 by peterkroon
Replied by peterkroon on topic Use of TNG to visualize a Martini trajectory
Hi Alfredo,

We compile VMD completely from scratch, which is kind of a pain. I don't know how to add plugins to a pre-compiled VMD. Have a look at the following webpages, and beyond that I'd refer you to the VMD mailinglist --- they seem like nice people ;)
Good luck!

www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/27764.html
www.ks.uiuc.edu/Research/vmd/plugins/molfile/
github.com/gromacs/tng

Peter

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4 years 11 months ago #8090 by alfredo
Replied by alfredo on topic Use of TNG to visualize a Martini trajectory
Hi Peter,
Thanks for the reply. Are there other visualization options to visualize Martini trajectories?
Best,

Alfredo

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4 years 11 months ago #8091 by riccardo
Replied by riccardo on topic Use of TNG to visualize a Martini trajectory
Yes, cg_bonds - see here: cgmartini.nl/index.php/rb

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4 years 11 months ago #8092 by alfredo
Replied by alfredo on topic Use of TNG to visualize a Martini trajectory
Hi Riccardo,
I have tried with cg_bonds. The script work only with old gromacs versions?
I have tried with gromacs 2016.3 and I get this error:

vmd > cg_bonds -gmx /home/alfredo/Software/gromacs-2016.3/build-gromacs/Install_GCC4p6/bin/gmx dump -tpr step7_production_moilgpu.tpr
can't read "molecules": no such variable

Thanks,
Alfredo

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4 years 11 months ago #8093 by riccardo
Replied by riccardo on topic Use of TNG to visualize a Martini trajectory
In the same page there's also a cg_bonds-v5.tcl, which works with GMX versions from 5 onwards (hence thus with 2016). Have you tried that?

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4 years 11 months ago #8094 by alfredo
Replied by alfredo on topic Use of TNG to visualize a Martini trajectory
cg_bonds-v5.tcl works. Thanks!

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