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On 7/11/2010 4:14 AM, Martin Kamp Jensen wrote:
<blockquote
cite="mid:AANLkTinD=yhAHBfdUTuFXRYezP=9RJ5dKJHpA-r07Zu0@mail.gmail.com"
type="cite">
<div class="gmail_quote">Hi Chris,</div>
<div class="gmail_quote"><br>
</div>
<div class="gmail_quote">On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof
Mlynarczyk <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:mitomaster@gmail.com">mitomaster@gmail.com</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;">Hi,<br>
<br>
You need to use md integrator for -rerun to work.<br>
</blockquote>
<div><br>
</div>
<div>Aha, now it seems to work. Thanks!</div>
<div><br>
</div>
<div>I am just sad that I did not find that information.
According to <a moz-do-not-send="true"
href="http://manual.gromacs.org/current/online/mdrun.html">http://manual.gromacs.org/current/online/mdrun.html</a> "With
-rerun an input trajectory can be given for which forces and
energies will be (re)calculated. Neighbor searching will be
performed for every frame, unless nstlist is zero (see the
.mdp file)."</div>
</div>
</blockquote>
<br>
Writing and documenting bulletproof software is tough work :-(<br>
<br>
I've fixed the code so that -rerun and EM or NM integrators flag a
fatal error.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTinD=yhAHBfdUTuFXRYezP=9RJ5dKJHpA-r07Zu0@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> </div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;"><br>
Good luck,<br>
Chris<br>
<br>
<div class="gmail_quote">2010/11/6 Martin Kamp Jensen <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:martin.kamp.jensen@gmail.com"
target="_blank">martin.kamp.jensen@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>
<div class="h5">Hello,
<div><br>
</div>
<div>Hopefully someone can help me understand how to
use the mdrun -rerun functionality, because
currently I am confused. I would like to be able to
look up potential energy values for a number of
conformations by calling mdrun -rerun once.</div>
<div><br>
</div>
<div>The idea to use mdrun -rerun is from advice given
to me by Mark Abraham on the gmx-developers list (<a
moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html</a> and <a
moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html</a>):</div>
<div><br>
</div>
<blockquote class="gmail_quote" style="margin: 0px 0px
0px 0.8ex; border-left: 1px solid rgb(204, 204,
204); padding-left: 1ex;">
You want GROMACS to find the energy of a potentially
infinite set of coordinates that appear magically,
and that is what mdrun -rerun does.</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px
0px 0.8ex; border-left: 1px solid rgb(204, 204,
204); padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px
0px 0.8ex; border-left: 1px solid rgb(204, 204,
204); padding-left: 1ex;">
The elegant way to do that is to write your series
of conformations to a pseudo-trajectory (in
whichever of GROMACS many trajectory formats is
convenient to you), and then invoke mdrun -rerun on
that trajectory with a suitable .tpr. Then you
either parse the .log file or the output .edr file
for the energies.</blockquote>
<div><br>
</div>
<div>I wanted to find out how this works so I have
been experimenting. I started out by looking at the
Peptide tutorial at <a moz-do-not-send="true"
href="http://manual.gromacs.org/current/online/speptide.html"
target="_blank">http://manual.gromacs.org/current/online/speptide.html</a>.
I used three different mdp files (integrator =
steep, nsteps = 0, 1, 2). This gave me three
conformations and their energy values. For testing
purposes I then wanted to get the energy values for
those three conformations using mdrun -rerun (and
since I already have the correct energy values it is
easy to verify the results).</div>
<div><br>
First, I created a trajectory by concatenating the
three conformations (gro files) into one gro file
(which is okay according to <a
moz-do-not-send="true"
href="http://manual.gromacs.org/current/online/gro.html"
target="_blank">http://manual.gromacs.org/current/online/gro.html</a>:
"gro files can be used as trajectory by simply
concatenating files"). I then used an mdp file with
integrator = steep and nsteps = 0 indicating that I
just want the energy value (listed in the output, in
the log file or by using g_energy). Now, by using
mdrun -s <tpr file> -rerun <gro trajectory
file> I only get the energy value for the first
conformation listed in the gro file used to create
the tpr file. The -rerun option does not seem to
have any effect at all.</div>
<div><br>
</div>
<div>I used the following commands three times to
create three different conformations (one
conf_mdrun.gro file for each time) with different
energy values. I am just setting nsteps to 0, 1, or
2 (integrator = steep) in em.mdp.</div>
<div><br>
</div>
<div>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx
-i top_pdb2gmx << EOF</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
1</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
1</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
EOF</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
editconf -f conf_pdb2gmx -o conf_editconf -d 0.5</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
genbox -cp conf_editconf -cs -p top_pdb2gmx -o
conf_genbox</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
mv top_pdb2gmx.top top_genbox.top</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
mv "#top_pdb2gmx.top.1#" top_pdb2gmx.top</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
grompp -f em -po em_grompp -c conf_genbox -p
top_genbox -o em_grompp</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px
0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun
-g mdrun</blockquote>
</div>
<div><br>
</div>
<div>I was hoping the following would give me the
three energy values for the three conformations in
2+1+0.gro, which is the concatenation of the three
conf_mdrun.gro files from before. However, I just
get the energy value from the first conformation in
the file. Using the -rerun option does not make a
difference (I can put whatever after -rerun, even
files that do not exist, without any effect).</div>
<div><br>
</div>
<blockquote class="gmail_quote" style="margin: 0px 0px
0px 0.8ex; border-left: 1px solid rgb(204, 204,
204); padding-left: 1ex;">
grompp -f em -po em_grompp -c gro/2+1+0 -p
top_genbox -o em_grompp</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px
0px 0.8ex; border-left: 1px solid rgb(204, 204,
204); padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px
0px 0.8ex; border-left: 1px solid rgb(204, 204,
204); padding-left: 1ex;">
mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro</blockquote>
<div><br>
</div>
<div>Regards,</div>
<div>Martin.</div>
<br>
</div>
</div>
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</div>
<br>
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</blockquote>
</div>
<br>
<div>Regards,<br>
</div>
<div>Martin.</div>
</blockquote>
<br>
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