[gmx-developers] Conformation representation and energy function

Martin Kamp Jensen martin.kamp.jensen at gmail.com
Tue Oct 5 16:37:09 CEST 2010

On Tue, Oct 5, 2010 at 4:02 PM, Axel Kohlmeyer
<akohlmey at cmm.chem.upenn.edu>wrote:

> martin,
> some general remarks. i'll try to be short, if you want, we can discuss
> more off-list, as this is really not so much of a development list issue.
> i suspect you are trying to put the horse before the cart here.
> before trying to find out the technical details, you should think
> (and discuss with your colleagues) some fundamental issues.
> what you describe would work only reasonably well for a peptide
> in vacuum (or implicit solvent). are you sure this is a useful piece
> of information? usually peptides are studies immersed in a solvent
> and then suddenly you cannot just move things around, as you
> would have to move the solvent as well (to make room). and on
> top of that, the useful information is the "free energy" i.e. some average
> that includes information about the statistical relevance (entropy)
> of the conformation you are looking at. there is plenty of literature
> on a variety of methods to map out free energy landscapes.
> if this is not a concern, you should still consider your approach.
> as was mentioned, using some external scripting is straightforward
> and will help you focus on implementing your method and testing
> its correctness, and then i would first try it on a simplified "toy" code,
> before trying to integrate something into a code base as large as
> gromacs. you have to be sure about what you need for your method,
> so that the only problems of merging are technical issues of understanding
> gromacs. otherwise you will be constantly confused by what is the
> origin of failures: your method? your implementation? or your integration
> into gromacs? if you don't have any practical experience in running
> an MD code and being able to tell whether it works correctly or not,
> how would you expect to be able to modify it correctly? large packages
> have lots of subtle issues and classical force field calculations have
> some surprises of their own and thus need some practice for the users
> until they are confident in judging its outcome.

I am doing preliminary work now to assess whether or not the approaches I
mentioned are feasible. I very much appreciate the comments from all of you
and I will certainly discuss them with my contacts.

Thanks a lot,

> cheers,
>     axel.
> On Tue, Oct 5, 2010 at 7:20 AM, Martin Kamp Jensen
> <martin.kamp.jensen at gmail.com> wrote:
> > Hello,
> > I would like to manipulate the conformation of a peptide inside of
> > 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.
> > --
> > gmx-developers mailing list
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> >
> --
> Dr. Axel Kohlmeyer    akohlmey at gmail.com
> http://sites.google.com/site/akohlmey/
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
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