normal Difficulties in Visualization of PDADMA30

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2 months 2 weeks ago #7714 by Ali
Ali created the topic: Difficulties in Visualization of PDADMA30
Hello,

I'm new to coarse-grained simulation. I have downloaded the example of polyelectrolyte-mixture and I'm trying to visualize it using VMD.
What I see are only dots and unusual chains. I tried cg_bonds.tcl but I think I'm doing something wrong.
I think I'm doing something wrong.
Please, can anyone tell me what I have to do? for better visualization

Thanks in advance

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2 months 1 week ago - 1 month 3 weeks ago #7721 by riccardo
riccardo replied the topic: Difficulties in Visualization of PDADMA30
Hi,

Not sure what you're doing wrong with cg_bonds.tcl - it should work.

However, with the latest versions of gromacs (2016 or higher, if I'm not wrong) there's a new file format for the trajectories: tng. This file format already contains topology information, i.e., you don't need the cg_bonds.tcl anymore!

So, you could try to do the following. Assuming that you downloaded the files from: cgmartini.nl/index.php/polyelectrolytes , you could run:

gmx grompp -p pe30-10-nacl-032-pw-818.top -c pe30-10-nacl-032-pw-818.gro -f martini_md.mdp

to generate a tpr, and then:

gmx trjconv -f pe30-10-nacl-032-pw-818.gro -o pe30-10-nacl-032-pw-818.tng -s topol.tpr

to generate the tng file. Now, you should be able to open this with vmd:

vmd pe30-10-nacl-032-pw-818.tng

and see the bonds connecting the beads automatically.
Last Edit: 1 month 3 weeks ago by riccardo.

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2 months 1 week ago #7724 by peterkroon
peterkroon replied the topic: Difficulties in Visualization of PDADMA30
You do need to have VMD compiled with the TNG plugin though, so YMMV.

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