hi i m doing simulation membrane protein while scaling down the lipids by a factor of 0.95 then performing EM
Steepest Descents converged to Fmax < 10 in 18 steps Potential Energy = -nan Maximum force = 4.7791553e+02 on atom 5440 Norm of force = -nan ; 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 = 10.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.1 ; Energy step size nsteps = 25000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; 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 = Shift ; 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 (yes/no) define = -DSTRONG_POSRES earlier when i was using ; 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 (yes/no) define = -DFLEXIBLE then problem was same help me ! with regards: shikha
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