normal Gromacs + Martini Error in Visualization = 'child process exited abnormally'

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1 year 8 months ago #9516 by bqAlvii
Hello community. I have a serious problem when I have to change the visualization of a short molecular dynamics made with martini CG. The problem occurs when executing the command to change the visualization in vmd using the tcl file cg_bonds-v5.tcl
The command should be executed by loading the tcl file to the tkconsole, through the following command =
cg bonds -gmx /usr/local/gromacs/bin/GMXRC/ -tpr mycoordinatesfile.tpr

The problem occurs when executing the command, I get this result =
(gromacs) 47 % cg_bonds -gmx /usr/local/gromacs/bin/GMXRC -tpr step7_production.tpr
going to dump tpr
variable tpr set
file11 child process exited abnormally

I read that it can be fixed by changing the gromacs file path, however it didn't work.
Any ideas?

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1 year 8 months ago #9518 by riccardo
In the top command you have an extra "/". Should be GMXRC (instead of GMXRC/) - maybe that's the problem?

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1 year 6 months ago #9545 by bqAlvii
Hi Riccardo.

Month ago i successfully performed a CG dynamics, in this case just only membrane lipids. I could visualize the structure using this command :
echo 0 | gmx trjconv -f 08.gro -s 08.tpr -conect -o run-conect.pdb -pbc whole
sed -i '/ENDMDL/d'  run-conect.pdb

But, in recent dynamics, i tried to use that command and couldn't achieve the correct visualization of my model, only obtaining dots. (in vmd, i change the representation to licorice)

Im doing something wrong?
There is another way to visualize my dynamics?

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1 year 6 months ago #9554 by riccardo
If it used to work a month ago for you, check what you changed from that one month ago system to what you're trying now step by step so you can find the root of the problem.

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