[gmx-users] Solvation of protein on membrane surface

[Olga Press]

Thanks a lot for your help.

‫בתאריך יום ב׳, 21 באוק׳ 2019 ב-19:51 מאת ‪Justin Lemkul‬‏ <‪jalemkul at vt.edu
‬‏>:‬

>
>
> On 10/20/19 5:57 AM, Olga Press wrote:
> > 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?
>
> A normal protocol with restraints on your protein should work fine.
> Those voids will be gone within tens of picoseconds.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
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-- 
*Olga Press-Sandler*
Ph.D. student, Yifat Miller's lab
Department of Chemistry
Ben-Gurion University, Israel