Thanks a lot for your help. בתאריך יום ב׳, 21 באוק׳ 2019 ב-19:51 מאת Justin Lemkul <jalem...@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 > > -- > ================================================== > > 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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Olga Press-Sandler* Ph.D. student, Yifat Miller's lab Department of Chemistry Ben-Gurion University, Israel -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.