[gmx-developers] Conformation representation and energy function

Anthony Costa anthony.costa at gmail.com
Tue Oct 5 15:40:52 CEST 2010

Dear Martin,

Just my two cents, but this is not something I would use Gromacs for.
There are many more robust ways of accomplishing what you're looking
for exactly. Have a look at the work of David Wales (Cambridge), and
his book entitled "Energy Landscapes: Applications to Clusters,
Biomolecules and Glasses". His program GMIN does *exactly* what you're
looking for in point (1), but means of either a markov-chain monte
carlo or a molecular dynamics-quenching within some forcefield. There
are tons of potentials built in, including some molecular forcefields
(AMBER), and it's not too hard to add your own.

The program GMIN does (doubly)-nudged elastic band calculations along
with a nice connection algorithm (see work of Trygubenko in the Wales
group) which can calculate minimum energy pathways between very
disconnected local minima, starting with structures revealed in GMIN.

The programs can be difficult to use, and I certainly can't provide
support, but there is extensive documentation online.

In any case I would begin to read the energy landscape literature
because many of the things you're suggesting here are well studied in
the literature and there exist many robust (and not-so-robust) methods
for calculating exactly these things. Wales's book is a great place to
start, it's where I started when I was doing this type of work.


On Tue, Oct 5, 2010 at 06:20, Martin Kamp Jensen
<martin.kamp.jensen at gmail.com> wrote:
> Hello,
> 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 http://www.gromacs.org/Developer_Zone/Programming_Guide/Data_Structures
> without 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.
> Regards,
> Martin.
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