[gmx-users] vibrational spectra of glucose

[Nilesh Dhumal]

I used the opls parameters in gromacs.
NIlesh

On Thu, May 27, 2010 1:17 pm, Erik Marklund wrote:
> 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/
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting! Please don't post (un)subscribe requests to the list. Use the
>>>  www interface or send it to gmx-users-request at gromacs.org. Can't
>>> post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>
>
> --
> -----------------------------------------------
> 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/
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>  Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
>