On 11/30/13 9:29 AM, jkrie...@mrc-lmb.cam.ac.uk wrote:
As has been asked a number of times before, I have seen minimization halt at a low number of steps having converged to machine precision when double precision is not used - does that not mean that double precision is needed at least for minimization? Sorry to ask this question again but I can't find a clear answer to this in previous messages.
That depends on the outcome. Consider the purpose of EM - to generate a reasonable structure that can be subjected to dynamics, the tolerance for which is user-defined in emtol. Sometimes the input structure requires very little change, so you reach an acceptable Fmax (e.g. emtol) within a very small number of steps. Double precision is only required when you are aiming for a very small Fmax, as would be necessary for, e.g. NMA calculations. For most dynamics, single precision is perfectly acceptable for all steps in the process.
If EM converges prematurely without achieving the desired Fmax, usually one of two things has happened. Either the input structure cannot be resolved (in which case the Epot and Fmax are obviously bad) or the Fmax cannot be achieved with the parameters being utilized, in which case *maybe* double precision will fare better. The question you have to ask is whether or not you need that level of Fmax.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. 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 ================================================== -- 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.
