hi <br><br>i m doing simulation membrane protein <br>while scaling down the lipids by a factor of 0.95 then performing EM <br><br>Steepest Descents converged to Fmax < 10 in 18 steps<br>Potential Energy = -nan<br>Maximum force = 4.7791553e+02 on atom 5440<br>
Norm of force = -nan<br><br><br><br>; minim.mdp - used as input into grompp to generate em.tpr<br>; Parameters describing what to do, when to stop and what to save<br>integrator = steep ; Algorithm (steep = steepest descent minimization)<br>
emtol = 10.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>emstep = 0.1 ; Energy step size<br>nsteps = 25000 ; Maximum number of (minimization) steps to perform<br>
<br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>nstlist = 10 ; Frequency to update the neighbor list and long range forces<br>ns_type = grid ; Method to determine neighbor list (simple, grid)<br>
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)<br>coulombtype = Shift ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.2 ; Short-range electrostatic cut-off<br>
rvdw = 1.2 ; Short-range Van der Waals cut-off<br>pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>define = -DSTRONG_POSRES<br><br><br>earlier when i was using <br><br>; minim.mdp - used as input into grompp to generate em.tpr<br>
; Parameters describing what to do, when to stop and what to save<br>integrator = steep ; Algorithm (steep = steepest descent minimization)<br>emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>
emstep = 0.01 ; Energy step size<br>nsteps = 50000 ; Maximum number of (minimization) steps to perform<br><br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>
nstlist = 1 ; Frequency to update the neighbor list and long range forces<br>ns_type = grid ; Method to determine neighbor list (simple, grid)<br>rlist = 1.2 ; Cut-off for making neighbor list (short range forces)<br>
coulombtype = PME ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.2 ; Short-range electrostatic cut-off<br>rvdw = 1.2 ; Short-range Van der Waals cut-off<br>pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>
define = -DFLEXIBLE<br><br><br>then problem was same <br><br><br>help me !<br><br>with regards:<br>shikha <br>