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

[Rodrigo Faccioli]

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?

[1] http://gitorious.org/protpred-peo/gromacs
[2]
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
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