[gmx-developers] Help to compute backbone angles during simulation
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jun 18 20:33:38 CEST 2010
On 2010-06-18 20.12, Rodrigo Faccioli wrote:
> David, thanks for your answer.
>
> I would like to know more details about your ideas to analyse cartesian
> space rather than dihedral space.
>
> I understand that sampling in dihedral space may contain some problems.
> However, it allows to exploit the search space with a lower computation
> time.
>
> The dihedral representation is common in Evolutionary Algorithms (EA)
> based on not only in its power of exploit the search space but also, in
> thesis, can select the best conformations because the worse
> conformations (superposition of atoms, for example) have greater energy
> value. So, these conformations have less change to be selected for new
> generation.
>
Exactly, it may be easier to generate non-sensical conformations using
dihedral angle confs. but they may be filtered out quickly as well. In
cartesian space one could do a lot of small steps that have no effect.
What is better in the end I'm not sure. You will have to test...
Programs like autodock also use a genetic algorithm in dihedral space,
and are deemed to be efficient, as long as the number of degrees of
freedom is low.
> Sorry if my explanation about dihedral representation in EA isn't
> enough. I'm computer scientist try understanding about some physical
> properties. I might make mistakes :-)
>
> Thanks in advance,
>
> --
> 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 Wed, Jun 16, 2010 at 6:08 PM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> On 6/16/10 8:04 PM, Rodrigo Faccioli wrote:
>
> Hi,
>
> We've been working with ProtPred-PEO-Gromacs project [1]. In general
> lines, this project is a implementation of NSGA-II algorithm in
> Gromacs
> to discover a minima energy of protein conformation . NSGA-II is a
> Multi-Objective Evolutionary Algorithm (MOEA).
>
> More specific in Gromacs implementation, this project is a
> multi-system
> as REMD simulation. However, the new protein conformations are
> obtained
> from genetic operators. In [2] there is a simple documentation
> wrote by
> me to publish the some project ideas about it.
>
> The integrator option is peo instead of md and its function is
> do_peo in
> md.c. This project is under development version. My genetic
> operators
> work with the protein backbone angles. This representation is
> common for
> MOEAs when is working with proteins.
>
> In this way, I've studied about g_dhi program. I found the dih_angle
> function in bondfree.c. This function computes all backbone angles
> storing them in t_xrama structure represented by xr variable.
>
> Because of my simulation is a multi-system, I have for each system
> (protein conformation) a trr file. I need ideas to help me to
> obtain my
> backbone angles without call g_dhi routines..
>
> I thought to compute the backbone angles in my integration function
> (do_peo) because it has all atoms. So, I want to call a function
> which
> computes the backbone angle of my protein such as:
> t_peo_phipsi compute_backbone(t_mdatoms *mdatoms).
>
> Any comments for a good way to do this? Or other ways?
>
>
> Look in src/gmxlib/bondfree.c to see how this is done internally
> when computing dihedral forces. You loop over the right structure to
> compute the dihedrals.
>
> But do you really want to do the sampling in dihedral space?
> There are many false minima in dihedral space that are forbidden by
> van der waals interactions. It might be easier to do it in cartesian
> space.
>
>
>
> [1] http://gitorious.org/protpred-peo/gromacs
> [2]
> https://docs.google.com/fileview?id=0ByNUaKmUm2WoNDRlZDkwYmYtNTBhMS00NGUwLWI1MDMtOWEzMjNmY2I4OGQ5&hl=en
> <https://docs.google.com/fileview?id=0ByNUaKmUm2WoNDRlZDkwYmYtNTBhMS00NGUwLWI1MDMtOWEzMjNmY2I4OGQ5&hl=en>
> <https://docs.google.com/fileview?id=0ByNUaKmUm2WoNDRlZDkwYmYtNTBhMS00NGUwLWI1MDMtOWEzMjNmY2I4OGQ5&hl=en
> <https://docs.google.com/fileview?id=0ByNUaKmUm2WoNDRlZDkwYmYtNTBhMS00NGUwLWI1MDMtOWEzMjNmY2I4OGQ5&hl=en>>
>
>
> Thanks in advance,
>
> --
> 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
>
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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