[gmx-users] vibrational spectra of glucose

[Nilesh Dhumal]

After energy minimzation, I visualized the pdb and all atoms are really
far  from each other.

NIlesh

On Thu, May 27, 2010 1:10 pm, Erik Marklund wrote:
> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
> --
> -----------------------------------------------
> 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/
>
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