[gmx-users] Solvation of protein on membrane surface

[Justin Lemkul]

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
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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