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Ran Friedman wrote:
<blockquote cite="mid4891CD72.2030108@bioc.uzh.ch" type="cite">
<pre wrap="">Inon Sharony wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Ran.
I looked up your suggestions, and got the following:
0. The parameters in the *.tpr file appear in " 0.00000000e+00 "
format. How can I tell if this is a float or double? Also, I could not
see if the position coordinates of the molecule appear in the *.tpr
file (and if so, if they are in double-precision). Where do the
coordinates appear? (in the *.gro file only?)
</pre>
</blockquote>
<pre wrap=""><!---->When you run gmxdump it should right e.g.:
</pre>
</blockquote>
correction: Should WRITE. <br>
<blockquote cite="mid4891CD72.2030108@bioc.uzh.ch" type="cite">
<pre wrap="">Reading file em.tpr, VERSION 3.3.3 (double precision)
As for the coordinates, you have e.g.:
x[ 0]={ 1.35920e+01, 1.80590e+01, 1.79780e+01}
x[ 1]={ 1.31410e+01, 1.77710e+01, 1.75260e+01}
x[ 2]={ 1.30070e+01, 1.78390e+01, 1.68430e+01}
This is double precision. In single precision you'd get only 3 digits,
and the rest will be zeroes.
</pre>
<blockquote type="cite">
<pre wrap="">1. I do not get any step*.pdb files after the mdrun. In fact, I skip
the *.pdb file altogether (using PRODRG). Could this be a problem?
</pre>
</blockquote>
<pre wrap=""><!---->It doesn't matter if you use pdb or gro. step*.pdb files are sometimes
given in the output when the system explodes.
It can be that the parameters from PRODRG are not exactly what you want
- you should compare with the force field paramters and charges, though
I'm not sure this can be the source of this behaviour.
</pre>
<blockquote type="cite">
<pre wrap="">2. The simulation is done in vacuo.
3. I examined the input *.gro file (as well as the single-precision
mdruns) using ngmx, and it looks great for those runs that work (i.e.,
single precision).
I will now try repeating the whole minimization-NormalMode process for
a simple diatomic, to see if I have any problems. Could you send a
working set of files for me to compare with? Assuming you've run
Normal Mode analyses in the past...
</pre>
</blockquote>
<pre wrap=""><!---->I'm not sure a diatomic system is good for this - not enough degrees on
freedom.
I'll send you an example made with GMX 3.2.1 - I'm not doing NMA too
often, but it should work.
</pre>
<blockquote type="cite">
<pre wrap="">
Thanks very much again,
Inon.
Quoting "Ran Friedman" <a class="moz-txt-link-rfc2396E" href="mailto:r.friedman@bioc.uzh.ch"><r.friedman@bioc.uzh.ch></a>:
</pre>
<blockquote type="cite">
<pre wrap="">Inon Sharony wrote:
</pre>
<blockquote type="cite">
<pre wrap=""> Hi Ran, thanks for the reply
I ran "make tests" after compiling with double precision, and it
</pre>
</blockquote>
</blockquote>
<pre wrap="">came
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">out fine.
Could it be that this, second, compilation might have caused some
problems -- I had GROMACS compiled in single-precision, and it
</pre>
</blockquote>
</blockquote>
<pre wrap="">worked
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">fine -- could compiling in double-precision after the initial
single-precision overrun some files? I'm not sure anymore...
Also, the grompp in double-precision works fine (no warnings,
</pre>
</blockquote>
</blockquote>
<pre wrap="">etc.)
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">but I get the segfault from mdrun (also in double-precision).
Sometimes this happens in the first minimization step, and
</pre>
</blockquote>
</blockquote>
<pre wrap="">sometimes
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">in the second. I was told that this might hint that the input
</pre>
</blockquote>
</blockquote>
<pre wrap="">file/s
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">(e.g. the *.gro file) were input in single- and not
</pre>
</blockquote>
</blockquote>
<pre wrap="">double-precision.
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">However, since the files have coordinates written in nanometers to
four significant digits, I can't see how the input numbers could
</pre>
</blockquote>
</blockquote>
<pre wrap="">be in
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">single or double precision. It was suggested that I insert a
</pre>
</blockquote>
</blockquote>
<pre wrap="">"print to
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">screen" line in the source code immediately after the *.gro file
</pre>
</blockquote>
</blockquote>
<pre wrap="">is
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">read, to see if the printed data is in single-precision or
double-precision format. What do you think?
</pre>
</blockquote>
<pre wrap="">The tpr should contain the data in double precision. You can check
</pre>
</blockquote>
<pre wrap="">this
</pre>
<blockquote type="cite">
<pre wrap="">with gmxdump.
Other things that you may want to consider:
1. Do you get step*.pdb files after running mdrun? This may point
</pre>
</blockquote>
<pre wrap="">out to
</pre>
<blockquote type="cite">
<pre wrap="">something wrong in the input.
2. Are you using a solvated system? Normally NMA is done in vacuo,
</pre>
</blockquote>
<pre wrap="">maybe
</pre>
<blockquote type="cite">
<pre wrap="">with some scaling of the dielectric.
3. Did you examine the system that you use in the input? Does it
</pre>
</blockquote>
<pre wrap="">make
</pre>
<blockquote type="cite">
<pre wrap="">sense to you?
Ran.
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</pre>
</blockquote>
<pre wrap="">posting!
</pre>
<blockquote type="cite">
<pre wrap="">Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
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</pre>
</blockquote>
<pre wrap="">--Inon Sharony
×× ×× ×©×¨×× ×
+972(3)6407634
atto.TAU.ac.IL/~inonshar
Please consider your environmental responsibility before printing
this e-mail.
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</pre>
</blockquote>
<pre wrap=""><!---->
_______________________________________________
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Please don't post (un)subscribe requests to the list. Use the
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Can't post? Read <a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a>
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.unizh.ch">r.friedman@bioc.unizh.ch</a>
Skype: ran.friedman
------------------------------------------------------
</pre>
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