On 3/6/17 10:16 AM, zeineb SI CHAIB wrote:
Dear Justin, Thank you very much for your help and clarifications. I have a question please: I used OPLS-3 force field when running my simulations with Desmond, which is absent in GROMACS 5.1.3 In order to generate the topology (protein and POPC), I guess I have to work with the same force field in GROMACS, OPLS-3. There is differences between OPLS3 and the OPLS that is implemented in GROMACS and I'm wondering if I can choose the latter when generating the topology and the rtp file for the analysis of my trajectories. May I have your opinion please?
None of the analysis methods you mentioned before will depend on the force field parameters. Very few analysis routines do, anyway. The force field is critical to determining the physical behavior during the simulation, not after it.
-Justin
Thank you in advance for your help. Best regards. Zeineb
-- ================================================== 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.
