[gmx-users] coarse grain dynamics

ram bio rmbio861 at gmail.com
Wed May 26 11:14:21 CEST 2010 

thanks all for the discussion.

On Tue, May 25, 2010 at 5:42 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Thanks for the comments and info, but is there any way to take a
>> particular  frame for eg. the last frame  of CG simulation and extend
>> the run into all-atom simulation further ...
>>
>
> There are tools out there to reconstruct an atomistic representation of a CG
> system (see link below, and poke around Google for a few minutes).  If you
> want to start a whole new simulation, that is certainly possible after (of
> course) regenerating your system topology to match the new system.
>
> -Justin
>
>> On Tue, May 25, 2010 at 5:32 PM, Jared James Thompson
>> <thompsjj at purdue.edu> wrote:
>>>
>>> I agree with Justin on this one. Simulations run using CG that is not
>>> optimized
>>> for reconstruction may not actually reflect the type of interactions you
>>> are
>>> looking for. The current result of this simulation may not directly
>>> correspond
>>> to a full atomistic result, so even if a reconstruction were performed
>>> you would
>>> most likely NOT be able to draw conclusions from it.
>>>
>>> Otherwise, everyone would run really fast simulations in CG, then
>>> reconstruct
>>> their systems afterward. :)
>>>
>>>
>>>
>>> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>>>
>>>>
>>>> ram bio wrote:
>>>>>
>>>>> thanks,
>>>>>
>>>>> but i am using gromacs version 4.0.07
>>>>>
>>>> I think the general consensus thus far is you won't be able to do what
>>>> you
>>>> want
>>>> without significant effort to reconstruct your system, and perhaps then
>>>> you
>>>> should question whether any tools that seek to build optimal hydrogens
>>>> from
>>>> CG
>>>> structures are going to bias the result.  Would those hydrogen bonds
>>>> have
>>>> actually formed in an AA simulation?  Hard to tell.  If you want to
>>>> analyze
>>>> hydrogen bonds, CG approximations are not probably sufficient.
>>>>
>>>> This is a good exercise in planning your analysis before conducting your
>>>> simulation.  You can probably estimate some sort of polar contacts from
>>>> your
>>>> CG
>>>> representation, but not hydrogen bonds.
>>>>
>>>> -Justin
>>>>
>>>>> On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi
>>>>> <egvega at gmail.com> wrote:
>>>>>>
>>>>>> Hi,
>>>>>> To change between representations (atomistic <--> coarse grained), if
>>>>>> you
>>>>>> are using the MARTINI FF, you can use the modified version of Gromacs
>>>>
>>>> 3.3,
>>>>>>
>>>>>> check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt
>>>>>> If you don't want to switch to full-atomistic representation, check
>>>>>> which
>>>>
>>>> CG
>>>>>>
>>>>>> atom types are able to form hydrogen bonds and look for interactions
>>>>
>>>> between
>>>>>>
>>>>>> them. Obviously, this will be an approximation.
>>>>>>
>>>>>> Esteban G. Vega-Hissi
>>>>>> UNSL
>>>>>> San Luis
>>>>>> Argentina
>>>>>> --
>>>>>> On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson
>>>>
>>>> <thompsjj at purdue.edu>
>>>>>>
>>>>>> wrote:
>>>>>>>
>>>>>>> There are programs around for reconstruction of full-atomistic
>>>>>>> representations
>>>>>>> from coarse-grained representations, however. I don't know if there
>>>>>>> are
>>>>>>> any
>>>>>>> available for the GROMACS architecture.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Quoting Nuno Azoia <nazoia at det.uminho.pt>:
>>>>>>>
>>>>>>>> Hi there!
>>>>>>>>
>>>>>>>> I never worked with coarse grain simulations, but if you used a
>>>>>>>> coarse
>>>>>>>> grain methodology you didn't include all the atoms, so you didn't
>>>>>>>> included hydrogens. So now you can not see them, of course. They are
>>>>
>>>> not
>>>>>>>>
>>>>>>>> there.
>>>>>>>>
>>>>>>>> If you need to "know the hydrogen bond interactions" you need to do
>>>>
>>>> some
>>>>>>>>
>>>>>>>> "all atoms" simulation, not coarse grain.
>>>>>>>>
>>>>>>>> Nuno Azoia
>>>>>>>>
>>>>>>>> On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:
>>>>>>>>>
>>>>>>>>> Dear Gromacs Users,
>>>>>>>>>
>>>>>>>>> I have done coarse grain simulation for 2 peptides in bilayer for
>>>>>>>>> 1000ns, and now i would like to know the hydrogen bond interactions
>>>>>>>>> between these two peptides. Please let me know how to do this, i
>>>>>>>>> can
>>>>>>>>> visualize the trajectory in VMD, but unable to calculate the
>>>>>>>>> hydrogen
>>>>>>>>> bonding distance and the hydrogen bonds existing..
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>>
>>>>>>>>> Ram
>>>>>>>>
>>>>>>>> --
>>>>>>>> Nuno Gonçalo Azoia Lopes
>>>>>>>>
>>>>>>>> Laboratório de Investigação em Acabamento
>>>>>>>> Departamento de Engenharia Têxtil
>>>>>>>> Universidade do Minho
>>>>>>>> Campus de Azurém
>>>>>>>> 4800-058 Guimarães
>>>>>>>> Portugal
>>>>>>>>
>>>>>>>> Tel: +351 253 510 280 - Ext: 517 289
>>>>>>>> Fax: +351 253 510 293
>>>>>>>>
>>>>>>>> Mobile: +351 965 382 487
>>>>>>>> E-mail: nazoia at det.uminho.pt
>>>>>>>> http://nazoia.net
>>>>>>>>
>>>>>>>> --
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>>>>>>>>
>>>>>>> --
>>>>>>> Jared James Thompson
>>>>>>> Department of Medicinal Chemistry and Molecular Pharmacology
>>>>>>> Laboratory for Computational Drug Design and Biology
>>>>>>> RHPH 504C
>>>>>>> Heine Pharmacy Building
>>>>>>> 575 Stadium Mall Drive
>>>>>>> West Lafayette, IN  47907-2091
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>>>>>>
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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
>>>>
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>>>
>>> --
>>> Jared James Thompson
>>> Department of Medicinal Chemistry and Molecular Pharmacology
>>> Laboratory for Computational Drug Design and Biology
>>> RHPH 504C
>>> Heine Pharmacy Building
>>> 575 Stadium Mall Drive
>>> West Lafayette, IN  47907-2091
>>> --
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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
>
> ========================================
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