normal Convert atomistic water to MARTINI

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3 months 1 week ago - 3 months 1 week ago #7730 by zidarko
zidarko created the topic: Convert atomistic water to MARTINI
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: 3 months 1 week ago by zidarko.

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3 months 1 week ago #7731 by riccardo
riccardo replied the 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 ).

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3 months 1 week ago #7732 by zidarko
zidarko replied the topic: Convert atomistic water to MARTINI
Thanks!

Let me try this route.

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