[gmx-users] coarse grain dynamics

[ram bio]

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 ...

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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>>
>> --
>> ========================================
>>
>> 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
> --
> gmx-users mailing list    gmx-users at gromacs.org
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