[gmx-users] vibrational spectra of glucose

[Nilesh Dhumal]

Hello,

I am trying to calculate the normal vibrational spectra of glcuose
molecule in vaccum. After the energy minimization,  I found all the bonds
are broken.
I have pasted the input file for energy minimzation.
WHy all bonds are geting broken.
Nilesh

define                   = -DFLEXIBLE

constraints              = all-bonds

integrator               = L-BFGS


nsteps                   = 15000

nbfgscorr                = 50

emtol                    = .001

emstep                   = 0.1

gen_vel                  = yes

gen-temp                 = 300

nstcomm                  =  1

; NEIGHBORSEARCHING PARAMETERS

; nblist update frequency

nstlist                  =10

; ns algorithm (simple or grid)

ns-type                  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)

pbc                      = no

; nblist cut-off

rlist                    = 0

domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype              = Cut-Off

rcoulomb-switch          = 0

rcoulomb                 = 0

; Dielectric constant (DC) for cut-off or DC of reaction field


; Method for doing Van der Waals

vdw-type                 = Cut-off

; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)

pbc                      = no

; nblist cut-off

rlist                    = 0

domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype              = Cut-Off

rcoulomb-switch          = 0

rcoulomb                 = 0

; Dielectric constant (DC) for cut-off or DC of reaction field


; Method for doing Van der Waals

vdw-type                 = Cut-off