hi > I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk . when i skiped scaling by factor 0.95 then , after EM step I m getting same potential energy nan result.
> 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 > Which version of Gromacs? On what hardware? I discovered a platform-specific bug that looked a lot like this, but I hesitate to suggest that until I know more. In all likelihood, you simply have unresolvable atomic overlap (i.e., you're packing too much) such that energy minimization cannot complete, since nan = "not a number," or something is infinitely large or small.
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