On 9/16/14 4:48 AM, Kester Wong wrote:
Dear gromacs team, I have recently converted a TIPS3P system (10k molecules) to a SWM4-NDP model. As I followed the instruction as listed below, I find it hard for beginners like me to convert the water structure: http://www.gromacs.org/Documentation/How-tos/Changing_a_3_Point_Water_Model_to_a_4_Point_Water_Model Notwithstanding, after doing some reading and tinkering on the .gro file formatting, and tinkering, I have managed to convert TIPS3P water to SWM4-NDP models. I find this technique very useful, as I think I could probably save some computing time by having the first few ns of the equilibration of SWM4-NDP model done in a less expensive way (e.g. 3-point water model). It can be applied for other water models too, e.g. TIP3P to TIP4P and TIP5P conversions.
I don't know that there's much to gain by doing such conversions. You still have to re-equilibrate no matter what, and the choice of TIP3P-equilibrated configuration is arbitrary; the final configuration of the simulation is not necessarily any better than any other snapshot, and you lose any semblance of continuity because you can't preserve the equilibrated ensemble of velocities, etc.
-Justin
I have devised a short step-by-step note that I think might be useful to other gromacs users. This could also be a good opportunity to update the web page with more information? Please let me know if this is okay, and I will send the notes as a doc. attachment? Regards, Kester
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
