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

[Olga Press (via Google Drive)]

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Solvation of protein on membrane surface .JPG
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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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