[gmx-users] Solvation of protein on membrane surface

[Olga Press]

Prof. Lemkul,
Thank you very much for your reply. I would be very grateful if you can
help me with some questions regarding voids compression.
Should I run the NPT equilibration on the whole system( including
protein+membrame+solvent +*ions*) meaning, should I continue my protocol
(adding ions-->NVT equilibration with position restraints on the
protein---> and than NPT equilibration with position restraints---> NPT
equilibration without restraints) or should I run first NPT
equilibration without position restraints (and for how long?) and than
continue the protocol?
Thanks alot!
Olga

‫בתאריך יום ב׳, 7 באוק׳ 2019 ב-18:23 מאת ‪Justin Lemkul‬‏ <‪jalemkul at vt.edu
‬‏>:‬

>
>
> 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
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> Virginia Tech Department of Biochemistry
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> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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-- 
*Olga Press-Sandler*
Ph.D. student, Yifat Miller's lab
Department of Chemistry
Ben-Gurion University, Israel