[gmx-users] Converting between cartesian coordinates and torsion angles

Martin Kamp Jensen martin.kamp.jensen at gmail.com
Sun Nov 14 18:13:27 CET 2010

Hi Mark,

Thanks (again, again) for your input!

On Fri, Nov 12, 2010 at 5:35 PM, Mark Abraham <Mark.Abraham at 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.

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.)

> to create input for your procedure.
> Mark
>  Regards,
> Martin.
>  [1] http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf
> [2]
> http://imada.sdu.dk/~mkjens04/gromacs/intra-molecular_interactions_definitions.png<http://imada.sdu.dk/%7Emkjens04/gromacs/intra-molecular_interactions_definitions.png>
> [3] http://imada.sdu.dk/~mkjens04/gromacs/part_of_top_file.png<http://imada.sdu.dk/%7Emkjens04/gromacs/part_of_top_file.png>
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