[gmx-users] Monte Carlo with Gromacs and implicit solvent

[Rodrigo Faccioli]

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.
>>      ------------------------------**-----------------------
>>      --
>>      gmx-users mailing list    gmx-users at gromacs.org
>>      http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>      Please search the archive at
>>      http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>      Please don't post (un)subscribe requests to the list. Use the www
>> interface or
>>      send it to gmx-users-request at gromacs.org.
>>      Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>>
>>
>>
>>
> ------------------------------**-----------------------
> 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.
> ------------------------------**-----------------------
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120124/aedd56b6/attachment.html>