[gmx-users] Fwd: removing some atoms

João Martins joaomartins139 at gmail.com
Mon Nov 30 09:56:13 CET 2015

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:


Like I said, for this specific case I would probably do it manually,
probably with Pymol. You can load both structures, and move the protein to
the desired position using the editing mode. Then, delete overlapping oil
atoms and save the structure.

Best regards,
João Martins

*Joao Martins*

joaomartins139 at gmail.com

On Mon, Nov 30, 2015 at 9:44 AM, James Lord <jjamesgreen110 at gmail.com>

> 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 <jjamesgreen110 at gmail.com>
> Date: Thu, Nov 26, 2015 at 11:18 PM
> Subject: removing some atoms
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Hi all,
> I have a oil slab and want to insert a protein so that almost half of the
> protein is inserted into the oil and the other half is outside in the
> vacuum. Is there any tools in Gromacs so that I can easily remove some of
> the oil atoms and make a space for the protein insertion? My apology if it
> seems a trivial question.
> Cheers,
> James
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