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

[David van der Spoel]

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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++