Re: [gmx-users] Fwd: removing some atoms

I am not sure how familiar with programming, but my usual approach is to simply insert the molecules and then write a program that removes the solvent residues whose atoms are too close to the protein. Another approach would be to use gmx solvate to solvate your protein as usual and then write a

[gmx-users] Fwd: removing some atoms

Hi all, I sent this few days ago and I am still struggling with this, any help,hints is highly appreciated. -- Forwarded message -- From: James Lord Date: Thu, Nov 26, 2015 at 11:18 PM Subject: removing some atoms To: "gmx-us...@gromacs.org"

Re: [gmx-users] Fwd: removing some atoms

There are some automated tools for membrane insertion that you can probably modify for you use, but I would probably just try a manual insertion followed by a long equilibration. For the membrane insertion you have this tutorial which uses InflateGRO: