Hi Mark,<div><br></div><div>Thanks (again, again) for your input!</div><div><br><div class="gmail_quote">On Fri, Nov 12, 2010 at 5:35 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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On 13/11/2010 12:49 AM, Martin Kamp Jensen wrote:
<blockquote type="cite"><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></div>
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.<div><br>
<br>
<blockquote type="cite"><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></div>
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</div></blockquote><div><br></div><div>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.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div text="#000000" bgcolor="#ffffff"> <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></div></blockquote><div><br></div><div>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.</div>
<div><br></div><div>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.)</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div text="#000000" bgcolor="#ffffff">
<br>
to create input for your procedure.<br><font color="#888888">
<br>
Mark</font><div><br>
<br>
<blockquote type="cite"><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 href="http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf" style="color:rgb(0, 0, 204)" target="_blank">http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf</a></div>
<div>[2] <a href="http://imada.sdu.dk/%7Emkjens04/gromacs/intra-molecular_interactions_definitions.png" target="_blank">http://imada.sdu.dk/~mkjens04/gromacs/intra-molecular_interactions_definitions.png</a></div>
<div>[3] <span style="border-collapse:separate;font-family:arial;font-size:small"><a href="http://imada.sdu.dk/%7Emkjens04/gromacs/part_of_top_file.png" target="_blank">http://imada.sdu.dk/~mkjens04/gromacs/part_of_top_file.png</a></span></div>
</span>
</blockquote>
<br>
</div></div>
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