[gmx-users] Solvation of protein on membrane surface

[Olga Press]

Dear all,
I would like to perform a simulation of protein on a membrane surface.
Following the placement of the protein on the DOPC surface I solvated 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 several water molecules are
"missing"  in the edges of the box. The image is attached to the mail.
Any suggestions for how can I solve the problem?
Thank you.

-- 
*Olga Press-Sandler*
Ph.D. student, Yifat Miller's lab
Department of Chemistry
Ben-Gurion University, Israel