[gmx-users] vibrational spectra of glucose

[Erik Marklund]

Where did you get the parameters for glucose? Those are my first suspects.

Erik

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


-- 
-----------------------------------------------
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/