On 1/20/16 11:16 PM, Alireza Moradzadeh wrote:
Dear Users, I want to simulate [BMIM][PF6] using following itp [ moleculetype ] PF6 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 P 1 PF6 P1 1 1.13 30.974 2 FP 1 PF6 F2 2 -0.33 18.998 3 FP 1 PF6 F3 3 -0.33 18.998 4 FP 1 PF6 F4 4 -0.33 18.998 5 FP 1 PF6 F5 5 -0.33 18.998 6 FP 1 PF6 F6 6 -0.33 18.998 7 FP 1 PF6 F7 7 -0.33 18.998 [ bonds ] 1 2 1 1 3 1 1 4 1 1 5 1 1 6 1 1 7 1 [ angles ] 2 1 3 1 2 1 4 1 2 1 6 1 2 1 7 1 3 1 4 1 3 1 5 1 3 1 7 1 4 1 5 1 4 1 6 1 5 1 6 1 5 1 7 1 6 1 7 1 2 1 5 1 180. 1165. 3 1 6 1 180. 1165. 4 1 7 1 180. 1165. But I get following errors for both of my molecules. Molecule type "PF" has 21 constraints. For stability and efficiency reasons there should not be more constraints more than internal degree of freedoms: 15 Is it right to use maxwarn in this case?!
You're being told that what you're trying to do (presumably via constraints = all-angles) is not physically stable. You can override this, of course, but then don't come asking for help when your simulation crashes. grompp already warned you :)
-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.
