Hi, Look at atom 380 and see why the forces might be high.
Mark On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <farideh.kham...@gmail.com> wrote: > Thank you for your great help on specbond.dat file. I defined it and I > could go ahead until Energy minimization step. I have used this minim.mdp > file > > ; minim.mdp - used as input into grompp to generate em.tpr > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steepest descent > minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < > 1000.0 kJ/mol/nm > emstep = 0.01 ; Energy step size > nsteps = 50000 ; Maximum number of (minimization) steps to > perform > > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > nstlist = 1 ; Frequency to update the neighbor list and > long range forces > ns_type = grid ; Method to determine neighbor list > (simple, grid) > rlist = 1.0 ; Cut-off for making neighbor list > (short range forces) > coulombtype = PME ; Treatment of long range electrostatic > interactions > rcoulomb = 1.0 ; Short-range electrostatic cut-off > rvdw = 1.0 ; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions (yes/no) > > But when I run mdrun -v -deffnm em command, I get this error: > > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 1000 (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. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 90 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -2.3956744e+05 > Maximum force = 1.5824519e+05 on atom 380 > Norm of force = 1.7695243e+03 > > gcq#187: "Been There, Done It" (Beavis and Butthead) > > farideh@farideh-P61A-D3:~/FARIDEH$ > > I changed the emtol, emstep, and nsteps for a few times. However, I > couldn't resolve this problem. Could you tell me if there is something > wrong with the minim.mdp file? > > You can see all the files via: > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 > > Truly yours, > Farideh > -- > 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. > -- 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.