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On 15/11/2010 4:13 AM, Martin Kamp Jensen wrote:
<blockquote
cite="mid:AANLkTims72PnBdjb6sxg+783oF2XzKqYBMfeLVjWN2uq@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff">
<div> 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: 0pt 0pt 0pt
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<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>
</div>
</blockquote>
<br>
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.
<a class="moz-txt-link-freetext" href="http://onlinelibrary.wiley.com/doi/10.1002/jcc.20237/abstract">http://onlinelibrary.wiley.com/doi/10.1002/jcc.20237/abstract</a>, and
many Google hits).<br>
<br>
<blockquote
cite="mid:AANLkTims72PnBdjb6sxg+783oF2XzKqYBMfeLVjWN2uq@mail.gmail.com"
type="cite">
<div>
<div class="gmail_quote">
<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>
<br>
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.<br>
<br>
Mark<br>
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