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On 13/11/2010 12:49 AM, Martin Kamp Jensen wrote:
<blockquote
cite="mid:AANLkTi=UFBMio7OaBOp0hbqpHJjhxuO3o_AV+gXKcRH3@mail.gmail.com"
type="cite"><span class="Apple-style-span" style="font-family:
arial,sans-serif; font-size: 13px; border-collapse: collapse;">Hi,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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?</div>
</span></blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:AANLkTi=UFBMio7OaBOp0hbqpHJjhxuO3o_AV+gXKcRH3@mail.gmail.com"
type="cite"><span class="Apple-style-span" style="font-family:
arial,sans-serif; font-size: 13px; border-collapse: collapse;">
<div><br>
</div>
<div>I have included screenshots of Table 5.5[2] and the
relevant part of some example .top file[3].</div>
<div><br>
</div>
<div>(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.)</div>
</span></blockquote>
<br>
Either <br>
<br>
a) write something that post-processes the result of grompp -pp in
concert with the same coordinate file to get the internal
coordinates, or <br>
<br>
b) use a hacked version of mdrun that writes internal coordinates
from within src/gmxlib/bondfree.c (probably used as mdrun -rerun) <br>
<br>
to create input for your procedure.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTi=UFBMio7OaBOp0hbqpHJjhxuO3o_AV+gXKcRH3@mail.gmail.com"
type="cite"><span class="Apple-style-span" style="font-family:
arial,sans-serif; font-size: 13px; border-collapse: collapse;">
<div><br>
</div>
<div>Regards,</div>
<div>Martin.</div>
<div><br>
</div>
<div>[1] <a moz-do-not-send="true"
href="http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf"
target="_blank" style="color: rgb(0, 0, 204);">http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf</a></div>
<div>[2] <a moz-do-not-send="true"
href="http://imada.sdu.dk/%7Emkjens04/gromacs/intra-molecular_interactions_definitions.png">http://imada.sdu.dk/~mkjens04/gromacs/intra-molecular_interactions_definitions.png</a></div>
<div>[3] <span class="Apple-style-span" style="border-collapse:
separate; font-family: arial; font-size: small;"><a
moz-do-not-send="true"
href="http://imada.sdu.dk/%7Emkjens04/gromacs/part_of_top_file.png">http://imada.sdu.dk/~mkjens04/gromacs/part_of_top_file.png</a></span></div>
</span>
</blockquote>
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