normal Convert atomistic water to MARTINI

  • zidarko
  • zidarko's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 months 5 days ago - 9 months 5 days ago #7730 by zidarko
Convert atomistic water to MARTINI was created by zidarko
Hello,

I'm trying to convert an atomistic system to a MARTINI one. I was able to convert the solute (not a protein or lipid) but I am facing major problems with converting the atomistic water into a coarse-grained representation. Let me emphasize I have a separate PDB for the solute and the solvent.

I tried to use VMD and its CG builder as a first approximation, but that doesn't work properly because it approximates a single molecule with one bead instead of lumping 3-4 molecules into one bead.

The martinize.py script ignores the water and does nothing. The relevant module CHARMM-GUI chokes as well.

I can visualize the solvent's all-atom PDB/GRO in VMD without a problem.

What to do?

Thanks in advance!

Jernej
Last edit: 9 months 5 days ago by zidarko.

Please Log in or Create an account to join the conversation.

More
9 months 5 days ago #7731 by riccardo
Replied by riccardo on topic Convert atomistic water to MARTINI
Hi Jernej,

Once you've coarse-grained the solute, just solvate the CG solute system with CG water using the gmx solvate command (it is done, for example, in the lipid tutorial at some point: cgmartini.nl/index.php/tutorials-general...n-gmx5/bilayers-gmx5 ).

Please Log in or Create an account to join the conversation.

  • zidarko
  • zidarko's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 months 5 days ago #7732 by zidarko
Replied by zidarko on topic Convert atomistic water to MARTINI
Thanks!

Let me try this route.

Please Log in or Create an account to join the conversation.

Time to create page: 0.094 seconds