[gmx-users] Monte Carlo with Gromacs and implicit solvent
Rodrigo Faccioli
rodrigo_faccioli at uol.com.br
Tue Jan 24 05:29:24 CET 2012
Hi Gianluca,
I forgot to say that the step of compute the energies is considered from
pdb2gmx until g_energy.
Sorry about my oblivion.
Best regards,
--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
On Tue, Jan 24, 2012 at 1:07 AM, Rodrigo Faccioli <
rodrigo_faccioli at uol.com.br> wrote:
> Hi Gianluca,
>
> Thanks your question.
>
> All steps to obtain a generation with 200 individuals, on average, is 6
> minutes for 1VII, example. In each generation I must converted my proteins
> Dihedral to Cartesian representation, compute the energies, choose the
> individuals which will go to reproduction, save previous population. This
> test was using one core of a conventional Desktop computer.
>
> The proteins, that I have tested my algorithm, vary from 20 to 56 amino
> acids.
>
> Best regards,
>
> --
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL
> Intelligent System in Structure Bioinformatics
> http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
>
>
> On Tue, Jan 24, 2012 at 12:36 AM, Gianluca Interlandi <
> gianluca at u.washington.edu> wrote:
>
>> Thanks Enrico!
>>
>> Just wondering. How fast is it? Calling gromacs must have a lot of
>> overhead. Also, do you call mdrun or does g_energy evaluate the energy?
>>
>> Gianluca
>>
>>
>> On Tue, 24 Jan 2012, Rodrigo Faccioli wrote:
>>
>> Hi,
>>>
>>> Although I don't work with MC simulation, I have used Gromacs to obtain
>>> energies and others
>>> protein features in my Evolutionary Algorithms (EA).
>>>
>>> In general lines, I created a script that calls Gromacs programs and the
>>> output of these
>>> programs, such as g_energy (I read its xvg file), I stored it at a
>>> specific file which is
>>> read by my algorithm and its values are put into my data structure. I
>>> call Gromacs either
>>> implicit or explicit solvent.
>>>
>>> My project is working with EA until now. However, the integration with
>>> GROMACS is able to
>>> work with other kind of algorithms such as MC. Actually, we have idea to
>>> work with MC. But,
>>> I don't know when it will be possible. If you want, we can talk about
>>> join these work.
>>>
>>> Best regards,
>>>
>>> --
>>> Rodrigo Antonio Faccioli
>>> Ph.D Student in Electrical Engineering
>>> University of Sao Paulo - USP
>>> Engineering School of Sao Carlos - EESC
>>> Department of Electrical Engineering - SEL
>>> Intelligent System in Structure Bioinformatics
>>> http://laips.sel.eesc.usp.br
>>> Phone: 55 (16) 3373-9366 Ext 229
>>> Curriculum Lattes - http://lattes.cnpq.br/**1025157978990218<http://lattes.cnpq.br/1025157978990218>
>>> Public Profile - http://br.linkedin.com/pub/**rodrigo-faccioli/7/589/a5<http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5>
>>>
>>>
>>> On Mon, Jan 23, 2012 at 11:39 PM, Gianluca Interlandi <
>>> gianluca at u.washington.edu> wrote:
>>> Hi!
>>>
>>> I would like to use gromacs to perform Monte Carlo simulations in
>>> implicit
>>> solvent of a protein near a surface. The protein is treated as a
>>> rigid body
>>> whereas the surface is fix.
>>>
>>> I see that there are plans to code MC into gromacs:
>>>
>>> http://www.gromacs.org/**Developer_Zone/Programming_**
>>> Guide/Monte_Carlo<http://www.gromacs.org/Developer_Zone/Programming_Guide/Monte_Carlo>
>>>
>>> Is there a preliminary version?
>>>
>>> If not, I wonder whether anybody has tried to do MC with gromacs
>>> using IMD and
>>> MDDriver:
>>>
>>> http://www.baaden.ibpc.fr/**projects/mddriver/<http://www.baaden.ibpc.fr/projects/mddriver/>
>>>
>>> Besides this. Is there an easy way to obtain the force field energy
>>> of a system
>>> using gromacs? Would I have to run a 0-steps MD and read out the
>>> energy? I know
>>> that this would have a big overhead in a MC simulation, but it
>>> might be worth
>>> trying.
>>>
>>> Thanks,
>>>
>>> Gianluca
>>>
>>> ------------------------------**-----------------------
>>> Gianluca Interlandi, PhD gianluca at u.washington.edu
>>> +1 (206) 685 4435
>>> http://artemide.bioeng.**washington.edu/<http://artemide.bioeng.washington.edu/>
>>>
>>> Postdoc at the Department of Bioengineering
>>> at the University of Washington, Seattle WA U.S.A.
>>> ------------------------------**-----------------------
>>> --
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>>>
>>>
>>>
>>>
>> ------------------------------**-----------------------
>> Gianluca Interlandi, PhD gianluca at u.washington.edu
>> +1 (206) 685 4435
>> http://artemide.bioeng.**washington.edu/<http://artemide.bioeng.washington.edu/>
>>
>> Postdoc at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> ------------------------------**-----------------------
>>
>> --
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>
>
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