[gmx-developers] Conformation representation and energy function

Martin Kamp Jensen martin.kamp.jensen at gmail.com
Tue Oct 5 13:20:23 CEST 2010


I would like to manipulate the conformation of a peptide inside of GROMACS.
More specifically, I want to add a method on the same level as do_steep,
do_nm, etc. (in mdlib/minimize.c) that repeatedly looks up the energy value
and in between changes the conformation of a peptide by changing the
dihedral angles. To be honest, I am overwhelmed by the data structures and
where to begin. I have looked at
any luck.

I am a computer science student that is about to do my master's thesis. That
plan is to, among other things, investigate the energy landscapes for
(small) peptides and create barrier trees. I will need to use the energy
function of GROMACS as a "black box", but of course I need to know how to
integrate with it. I have no knowledge of biochemistry :) (My contacts do,
of course...)

My goals are as follows.

1) Find as many local minima as possible in the energy landscape of a
(small) peptide. This could probably be implemented in an external program
that calls GROMACS multiple times as the energy minimization features
promise to find a local mimima close to the starting conformation. Another
possibility would be to integrate this functionality in GROMACS and then
maybe write the local minima to a trajectory file and read them in later for
use in 2). (How to know that I found all the local minima/the search is
converged will be one of my challenges.)

2) Find a way to "connect" pairs of local minima, i.e., what is the lowest
barrier connecting a pair of local minima. This is to be done using
heuristics to change one conformation to another (change the dihedral
angels) step by step. (Of course, the heuristics will be another one of my
challenges.) However, to do this, I will need to call the energy function
(evaluate_energy in mdlib/minimize.c) each time I change a conformation to
guide the heuristics. I am aware that changing the conformation after
GROMACS (mdrun) has parsed the binary run input file will probably remove
the possibility of using MPI because data has been distributed in some
specific way (maybe it is also a problem when using multiple threads on the
same machine). I will just have to accept that for now and then maybe in the
future look into the possibility of redistributing data after changing a
conformation. However, right now I do not even know how to change the
conformation/the dihedral angles...

So, in conclusion, I have some computer science challenges which will be my
focus, but I cannot get to them without some knowledge of GROMACS. I hope
someone will be able to give me some pointers.

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