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Use of TNG to visualize a Martini trajectory
- alfredo
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4 years 11 months ago #8087
by alfredo
Use of TNG to visualize a Martini trajectory was created 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
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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- peterkroon
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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
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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- alfredo
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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
Thanks for the reply. Are there other visualization options to visualize Martini trajectories?
Best,
Alfredo
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- riccardo
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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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- alfredo
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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
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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- riccardo
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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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- alfredo
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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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