Dear GMX users, I am facing problem while doing energy minimization before the molecular dynamic simulation step of a system consisting of protein, membrane, water and 14 ions.
The minim.mdp file is as follows ------------------------------------------------------------------------------------------------------------- ; 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 = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions * --------------------------------------------------------------------------------------------------------- * when I run this using the command * * *grompp –f minim.mdp –c system_sol_ions.gro -p topol.top –o em.tpr * then I invoked mdrun which gave following error -------------------------------------------------------------------------------------------------------- Reading file topol.tpr, VERSION 4.0.7 (single precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step= 14, Dmax= 1.2e-06 nm, Epot= 3.03531e+22 Fmax= inf, atom= 1417 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = 3.0353124e+22 Maximum force = inf on atom 1417 Norm of force = inf ----------------------------------------------------------------- After this I changed the emstep = 0.1 ; Energy step size nsteps = 5000 ; Maximum number of (minimization) steps to perform constraints = none After these changes the no of steps increased to 18 but still the system did not converge and potential energy is very high ---------------------------------------------------------------------------------------------------------- Reading file em.tpr, VERSION 4.0.7 (single precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 5000 Step= 17, Dmax= 1.5e-06 nm, Epot= 3.03531e+22 Fmax= inf, atom= 1417 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax < 1000. Potential Energy = 3.0353124e+22 Maximum force = inf on atom 1417 Norm of force = inf ---------------------------------------------------------------------------------------------------------------- What changes can I do in my minim.mdp file to converge my system and get a negative value of Epot. The topol.top file looks -------------------------------------------------------------------------------------------------- [ system ] ; Name protein 128-Lipid DPPC Bilayer [ molecules ] ; Compound #mols Protein_A 1 DPPC 121 SOL 11107 CL- 14 ----------------------------------------------------------------------------------------------------- Thanks, Parul
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
