[gmx-developers] Help to compute backbone angles during simulation
Rodrigo Faccioli
rodrigo_faccioli at uol.com.br
Fri Jun 18 23:42:39 CEST 2010
Actually, I have intention to combine both search strategies: dihedral and
cartezian.
I had developed my main loop and I committed it in my repository [1].
Please, look for do_peo function.
However, I'm developing the dihedral computation.
By the way, the pseudo code of my main loop can be see below:
while(generation<ngenerations)
{
if (generation > 0){
bRerun = TRUE;
}
while(step<nsteps){
dd_partition_system(): redistribute atoms every neighbor search
steps, calls atoms2md() with index
do_force(): calculate forces (bonded and nonbonded) acting on the
(home) atoms (no position update here)
write_traj(): write current coordinates to trajectory file (gathers
coordinates before hands if MPI-enabled)
update(): tcoupl, constraints, second part of leap frog, update X
coords
step++;
}
//Call Evolutionary Algorithm (NSGA-II) to build new conformation based
on the energy of conformations. Only here, we'll work with dihedral angles.
I'm working here.
buildnewconformation();
//According fitness values choose the best solution (conformation).
write_traj(): write current coordinates to trajectory file from best
solution
generation++
}
Thanks in advance,
[1] http://gitorious.org/protpred-peo/gromacs/blobs/master/src/kernel/md.c
--
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 Fri, Jun 18, 2010 at 3:33 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:
> 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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