[gmx-users] coarse grain dynamics

[ram bio]

thanks,

but i am using gromacs version 4.0.07

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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