On 15/11/2010 4:13 AM, Martin Kamp Jensen wrote:
Hi Mark,
Thanks (again, again) for your input!
On Fri, Nov 12, 2010 at 5:35 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 13/11/2010 12:49 AM, Martin Kamp Jensen wrote:
Hi,
As far as I understand, a topology (a .top file) and a
conformation (e.g., a .gro file) contain enough information to
calculate the torsion angles of that specific conformation.
Table 5.5 (page 124) in the GROMACS manual[1] describes possible
interactions (which are contained in the topology) between
different molecules while the conformation contains the cartesian
coordinates. I did not immediately find a way to convert between
the cartesian coordinates and the torsion angles. Can GROMACS do
it or do I need to understand (or just find) all the
functions/formulas that are referenced in Table 5.5?
Section 4.2 has the relevant definitions. Table 5.5 pertains to
the definition of force field elements that act upon (for example)
such internal coordinates, which is not what you're looking for.
I have included screenshots of Table 5.5[2] and the relevant part
of some example .top file[3].
(Also, it seems that I can use the read_tpx method defined in
include/tpxio.h to read in a topology from a .tpr file. This
would then, after converting the cartesian coordinates of some
conformation, enable me to work with the torsion angles in my own
program before writing cartesian coordinates back for use with
GROMACS.)
Either
a) write something that post-processes the result of grompp -pp in
concert with the same coordinate file to get the internal
coordinates, or
Okay, I see that grompp -pp generates a .top file with a lot of
parameters (and maybe even some angles), but for some reason atom
numbers have been exchanged with atom names, but of course I can
change that back. Then I would need to apply the math from Section 4.2
together with a specific conformation to get the angles (and then do
the math to get back to cartesian coordinates after having played with
the angles... hmm). Unless my contacts tell me that only a few of
those interactions will be needed for our purposes, this seems to be
unnecessary extra work.
b) use a hacked version of mdrun that writes internal coordinates
from within src/gmxlib/bondfree.c (probably used as mdrun -rerun)
This could be fine since I will only need to go from cartesian
coordinates to angles once. However, I will need to go from angles to
cartesian coordinates many, many times. And I would need to write
"inverse methods" since the methods in bondfree.c calculate angles
from cartesian coordinates to use them for force and energy calculations.
It seems to me that a better way of thinking/describing about what you
want to do is to convert something to an internal coordinate
representation, then do some operations on that, and then rebuild the
Cartesian coordinates for GROMACS. All of that is best done by pretty
much anything you can think of, rather than GROMACS (not least because
you may have to rebuild the solvent and whatever else goes along with
the changed internal coordinates). There is a body of literature and
software that deals with this problem, which is of interest to many
areas of computational chemistry (e.g.
http://onlinelibrary.wiley.com/doi/10.1002/jcc.20237/abstract, and many
Google hits).
Or am I missing something - is it possible to let GROMACS work on
angles instead of cartesian coordinates? (I mean give the input not
as, e.g., a .gro file with cartesian coordinates, but as another file
with torsion angles - which I will first get via bondfree.c.)
No, GROMACS will only accept Cartesian input. While it is well known
that geometry optimization is best done in (redundant) internal
coordinates when the evaluation of energy and/or force is expensive
(e.g. quantum chemistry on small systems), this is not true for the
large majority of EM problems on biomolecular systems. There, the
problem is dominated by the presence of multiple minima, the result is
not of great interest if you're preparing a system for MD, and there is
no payoff for the development time. Thus, GROMACS only computes an
internal coordinate immediately before using it to evaluate its
contribution to bonded energy and/or force, and then discards it.
Mark
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