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normal Visualization using VMD (Self-assembly of functionalized alkanes on a graphite)

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3 years 8 months ago - 3 years 8 months ago #8663 by Daisuke
Visualization using VMD (Self-assembly of functionalized alkanes on a graphite) was created by Daisuke
I successfully completed the MD simulation of the tutorial using GROMACS 16.6.

However, for the purpose of the visualization using VMD, I have the error massages as below:
1. “vmd> cg_bonds -gmx /wherever/gmxdump/ -tpr 3_run.tpr -net "elastic" -cutoff 12.0 -color "orange" -mat "AM25" -res 12 -rad 0.1
going to dump tpr couldn't excute "/wherever/gmxdump" : no such file or directory”

Thus, I edited cg_bonds-v5.tcl file (line 504) as:
set gmxdump "/usr/bin/gmx"-> "/usr/local/gromacs/bin/gmx"

After this, I got the messages as below:
2. “vmd > cg_bonds -top topol.top -topoltype "elastic"
Error: file /../FF/martini_v2.15.itp does not exist.”

I see by the finder that martini_v2.15.itp exists in the folder FF. What should I do next?


Thanks a lot in advance for anyone who can help me with these!
Last edit: 3 years 8 months ago by Daisuke.

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3 years 8 months ago #8670 by Daisuke
Replied by Daisuke on topic Visualization using VMD (Self-assembly of functionalized alkanes on a graphite)
I succeeded in the CG bond representation by input to the Tkconsole as:
"cg_bonds -tpr 3_run.tpr"

Thank you very much!

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  1. General topics
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  5. Visualization using VMD (Self-assembly of functionalized alkanes on a graphite)
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