[gmx-users] Solvation of protein on membrane surface .JPG

[Dallas Warren]

A visual artefact of the periodic boundary condition.

See https://twitter.com/dr_dbw/status/909559339366572032

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Mon, 7 Oct 2019 at 18:24, Olga Press (via Google Drive) <
drive-shares-noreply at google.com> wrote:

> I've shared an item with you:
>
> Solvation of protein on membrane surface .JPG
>
> https://drive.google.com/file/d/1cdYTCn7PLrRrt4aUSHz40WTLG7QZ9xzP/view?usp=sharing&ts=5d9ae82d
>
> It's not an attachment -- it's stored online. To open this item, just
> click
> the link above.
>
> Dear all,
> I would like to simulate a protein on membrane surface.
> Following the placement of the protein on the DOPC surface I solvate the
> system by the following command:
> gmx_mpi solvate -cp min_dopc.gro -cs spc216.gro -o solvate.gro -p
> system.top I made a local copy of vdwadii.dat were I set the C radius to
> 0.375 to avoid the penetration of water into the hydrophobic region.
> However, following the solvation it seems that the water molecules
> are "missing" in the edges of the box. I shared the image with the
> mailing
> list.
> Any suggestions?
> Thank you.
> Olga
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