Difficulties in Visualization of PDADMA30
- Ali
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5 years 9 months ago #7714
by Ali
Difficulties in Visualization of PDADMA30 was created by Ali
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
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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- riccardo
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5 years 9 months ago - 5 years 8 months ago #7721
by riccardo
Replied by riccardo on 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.
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: 5 years 8 months ago by riccardo.
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- peterkroon
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5 years 9 months ago #7724
by peterkroon
Replied by peterkroon on topic Difficulties in Visualization of PDADMA30
You do need to have VMD compiled with the TNG plugin though, so YMMV.
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