[gmx-users] Monte Carlo with Gromacs and implicit solvent
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Jan 24 10:21:38 CET 2012
On 24/01/2012 3:29 PM, Rodrigo Faccioli wrote:
> Hi Gianluca,
>
> I forgot to say that the step of compute the energies is considered
> from pdb2gmx until g_energy.
If your topology is not changing, then you need only construct a new
pseudo-trajectory for the n configurations whose energy you want, and
then run mdrun -rerun using the same .tpr every time. Even if the
topology can change, for doing lots of iterates, some kind of hash will
allow you to reuse previously generated .tpr files very cheaply.
Mark
>
> 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 <mailto: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 <mailto: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
> Public Profile -
> 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
> <mailto: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
>
> 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/
>
> 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
> <mailto:gianluca at u.washington.edu>
> +1 (206) 685 4435 <tel:%2B1%20%28206%29%20685%204435>
> 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
> <mailto:gianluca at u.washington.edu>
> +1 (206) 685 4435 <tel:%2B1%20%28206%29%20685%204435>
> 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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