On 8/3/15 6:38 PM, 折晓会 wrote:
Dear professor Justin, Thank you very much for your suggestions! I really appreciate your help! I build a larger system and use the parameters you suggested. The simulation is working better now, especially after decreasing the time step, but EM occasionally does not converge in some steps during the simulation. For example, step 341262: EM did not converge in 100 iterations, RMS force 2.608 step 341263: EM did not converge in 100 iterations, RMS force 15.730 step 341264: EM did not converge in 100 iterations, RMS force 40.663 step 341265: EM did not converge in 100 iterations, RMS force 88.519 step 341266: EM did not converge in 100 iterations, RMS force 173.432 step 473594: EM did not converge in 100 iterations, RMS force 9.094 step 473595: EM did not converge in 100 iterations, RMS force 24.042 step 473596: EM did not converge in 100 iterations, RMS force 57.226 step 473597: EM did not converge in 100 iterations, RMS force 127.469 step 473598: EM did not converge in 100 iterations, RMS force 285.591 step 473599: EM did not converge in 100 iterations, RMS force 479.862 I am wondering if this is common for polarizable model simulations. I tried to use different time steps (0.2, 0.5 and 0.8 fs) and longer steps (500 000, 800 000), but the similar warnings occured periodically as above. In addition, I am also confused about the outcome of the energy minimization, since it reaches neither the emtol (1) nor the nsteps (50000): Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Steepest Descents converged to machine precision in 2115 steps, but did not reach the requested Fmax < 1. Potential Energy = -1.0560062e+09 Maximum force = 1.7716933e+15 on atom 2483 Norm of force = 4.9991217e+13 Based on this outcome, is it due to the low machine precision which stops the energy minimization?
No, there's something catastrophically wrong with your system. The maximum force is 10^15! There's no point in doing dynamics with such a system. Either the topology is somehow incorrect or the starting coordinates are unreasonable such that they cannot be fixed with EM.
-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 [email protected] | (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 [email protected].
