[gmx-users] vibrational spectra of glucose

[Erik Marklund]

Bonds don't break in gromacs without qm/mm ...yet. Why do you think 
they're broken?

Erik

Nilesh Dhumal skrev:
> 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
>
>
>
>
>
>
>
>
>
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>   


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/