[gmx-users] vibrational spectra of glucose

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> I used the opls parameters in gromacs.

...and what parameters would those be?  I don't know of any "standard" glucose 
parameters that are included in the Gromacs distribution, at least not for OPLS-AA.

Also, what was the outcome of energy minimization?  Did it converge?  Did it 
crash?  Why are you using such a large emstep?  I suspect that 0.1 may lead to 
instability.

-Justin

> 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
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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/
>>
>> --
>> 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!
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>>
>>
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================