[gmx-users] coarse grain dynamics

Tue May 25 17:32:28 CEST 2010

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