[gmx-users] elastic network model - normal mode analysis

[mohan maruthi sena]

Hi all,
           I want to  do normal mode  analysis for a protein using elastic
network model containing 691 residues. I consider only c-alpha atoms
connected by a spring constant of 81600 kj/nm2.  When I do normal mode
analysis I  get the following error :

Maximum force: 6.30230e+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.
Finished step 691 out of 691

I have minimised the structure , still i get the same error. I use  in
gromacs 4.5.5 double precision  for  these simulations. When I load the
trajectory eigen.trr  in vmd(to see normal modes) , I could see the protein
far away and all atoms overlapped. I use the following .mdp file parameters
as input

; RUN CONTROL PARAMETERS
integrator               = nm
dt                       = 0.002 ; time step (ps)
nsteps                   = 1000000 ; number of steps


; OUTPUT CONTROL OPTIONS
nstenergy                = 500
nstxout                  = 500
nstvout                  = 500
nstfout                  = 500
energygrps               = System


; NEIGHBORSEARCHING PARAMETERS
nstlist                   = 0      #Frequency to update neighbourlist

pbc                       = no

comm_mode                 = ANGULAR

; OPTIONS FOR ELECTROSTATICS AND VDW

; Temperature coupling
tcoupl                   = v-rescale           ; Couple temperature to
external heat bath according to Berendsen method
tc-grps                  = System  ;Non-Protein ; Use separate heat baths
for Protein and Non-Protein groups
tau_t                    = 0.2      ;0.2         ; Coupling time constant,
controlling strength of coupling
ref_t                    = 300        ; Temperature of heat bath


; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  =  no   ; Assign velocities to particles by taking
them randomly from a Maxwell distribution
gen_temp                 = 300.0  ; Temperature to generate corresponding
Maxwell distribution
gen_seed                 = 9999   ; Seed for (semi) random number
generation. Different numbers give different sets of velocities

; OPTIONS FOR BONDS
constraints              = none ; No constraints except for those defined
explicitly in the topology

refcoord_scaling         = com

Please suggest me a way to rectify this error.



Thank you in advance,
Mohan.