[gmx-users] coarse grain dynamics

Tue May 25 17:42:47 CEST 2010

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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>>> --
>>> ========================================
>>>
>>> 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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>>
> 

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

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

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