On 2/4/14, 9:43 PM, Sidath Wijesinghe wrote:
yes it worked. i only added CA CA CZ CZ 0.000 0.000 0.000 0.000 in diheadral block. since all 12 errors point the same kind of diheadral type.
How did you decide these parameters were appropriate? You're essentially saying that the rotational barrier to this dihedral is zero, so it is free to do anything it likes without consequence. That's as useful as deleting the dihedral entirely.
Then i tried to mdrun...i got this error message.... Fatal error: 1 particles communicated to PME node 6 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. so i followed the energy minimization steps given in the lysozyme tutorial... and ended up with vales like below... Steepest Descents converged to Fmax < 1000 in 56 steps Potential Energy = 8.3839850e+02 Maximum force = 9.7320355e+02 on atom 206 Norm of force = 1.8842863e+02 there you have clearly stated that the potential energy should be in range of e-5 to e-6. but mine is ~+1000. i played with emsteps and nsteps. but still am getting the same potential energy.
For a condensed-phase system of an average protein in water, yes, the potential energy I report there is fairly typical. Don't try to extrapolate this information too far. For a condensed phase system, the potential is dominated by water-water interactions, driving the energy down. Your mileage will vary depending on what you're dealing with.
could you please help me out with this?
You need to parametrize the missing dihedral appropriately. Placeholder values are as useful as deletion (they're not), so you need to invest time in building a sound force field model.
-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 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.
