Difficulties in Visualization of PDADMA30
- Ali
-
Topic Author
- Visitor
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
Please Log in or Create an account to join the conversation.
- riccardo
-
- Offline
- Platinum Boarder
Less
More
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.
Please Log in or Create an account to join the conversation.
- peterkroon
-
- Offline
- Gold Boarder
Less
More
- Posts: 210
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.
Please Log in or Create an account to join the conversation.
Time to create page: 0.106 seconds