[gmx-developers] Help to compute backbone angles during simulation

[Rodrigo Faccioli]

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.

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>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
>> >
>>
>>
>> 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    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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