[gmx-users] Potential Energy = -nan

[shikha agarwal]

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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