[gmx-users] Solvation of protein on membrane surface

[Justin Lemkul]

On 10/7/19 3:30 AM, Olga Press wrote:
> 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?

Run a short NPT equilibration and the voids will compress.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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