[gmx-users] about normal mode analysis

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Dear users,

I'm trying to do NMA of a structure. When I minimize a structure:

Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 3742 steps
Potential Energy  = -5.2965824e+04
Maximum force     =  8.0245171e+00 on atom 3038
Norm of force     =  1.3228445e+00

When I try to perform a normal mode analysis:
Maximum force: 8.71126e+02
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.

I've seen some comments on this but I couldnt find any thing about its
solution. Anyone could give me any suggestions? Are there anyting wrong
with my input files?
By the way, I am using Gromacs 4.5.5.

Commands:
pdb2gmx -f protein.pdb -o protein.gro -p protein.top
14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
Select the Water Model:
4: SPC    simple point charge

editconf -f protein.gro -o protein-solvated.gro -bt dodecahedron -d 1.0

grompp -v -f minim.mdp -c protein-solvated.gro -p protein.top -o
protein-EM-solvated.tpr
mdrun -v -deffnm protein-EM-solvated

grompp -v -f nm.mdp -c protein-EM-solvated.gro -p protein.top -o
protein-nm.tpr
mdrun -v -deffnm protein-nm

Input files:

minim.mdp:
integrator    = cg        ; Algorithm (steep = steepest descent
minimization)
emtol        = 10.0      ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps        = 100000      ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist        = 0        ; Frequency to update the neighbor list and long
range forces
rlist        = 0        ; Cut-off for making neighbor list (short range
forces)
rcoulomb    = 0        ; Short-range electrostatic cut-off
rvdw        = 0        ; Short-range Van der Waals cut-off
pbc        = no         ; Periodic Boundary Conditions (yes/no)
constraints     = none

nm.mdp:
integrator    = nm
nsteps          = 500000  ; 1ns
dt              = 0.002     ; 2 fs

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist        = 0        ; Frequency to update the neighbor list and long
range forces
rlist        = 0        ; Cut-off for making neighbor list (short range
forces)
rcoulomb    = 0        ; Short-range electrostatic cut-off
rvdw        = 0        ; Short-range Van der Waals cut-off
pbc        = no         ; Periodic Boundary Conditions (yes/no)
constraints    = none


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