On 6/7/17 12:50 PM, ZHANG Cheng wrote:
Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models?
It is as Joao has said - that's just a coordinate file of a pre-equilibrated box of water that was generated using the SPC water model. You can indeed use it to simulate other 3-point water model systems following an initial equilibration.
I am trying to see if my protein will be denatured in cold condition.
The properties of the water model are going to be critical here. For instance, SPC has a maximum density around -41 C, which is obviously very unphysical (water has a real maximum density at +4 C) so if you're seeking to model behavior at -40 C, then SPC is a very bad choice because its properties are not realistic. I suggest you investigate the many possible water models that exist and find one or more that might reproduce some of the most important properties. None of them gets everything right.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
