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If I understood you correctly, you wanted to have different random
orientations of the molecules around your protein. To get N different
orientations, you should run genbox N times with N different seeds.<br>
<br>
Ran.<br>
<br>
Shay Amram wrote:
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<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial; color: windowtext;">Greetings
Ran,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial; color: windowtext;">I
tried to add the –seed flag as
you said, at the end of each genbox (with different various numbers),
and it doesn’t
help.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">(ran the following
command:)<o:p></o:p></span></font></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">genbox
-cp cent_tim.gro -ci plm.gro -nmol 4 -o 1PLM_tim.gro<u1:p></u1:p> –seed
4<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;">Each time I change the number
after “-seed”
I get a different GRO file,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;">But no matter how many time I
run genbox with the same
number after “-seed” I always get the same GRO file in the end.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;">Is it possible that there’s
something wrong in
the system settings? Something that has to do with the way genbox
chooses
random numbers?<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;">Thanks,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;">-Shay<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial; color: windowtext;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial; color: windowtext;"><o:p> </o:p></span></font></p>
<div>
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color="black" face="Times New Roman" size="3"><span
style="font-size: 12pt; color: windowtext;">
<hr tabindex="-1" align="center" size="2" width="100%"></span></font></div>
<p class="MsoNormal"><b><font color="black" face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma; color: windowtext; font-weight: bold;">From:</span></font></b><font
color="black" face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma; color: windowtext;">
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-freetext" href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>] <b><span
style="font-weight: bold;">On
Behalf Of </span></b>Ran Friedman<br>
<b><span style="font-weight: bold;">Sent:</span></b> Tuesday,
September 18, 2007
14:40<br>
<b><span style="font-weight: bold;">To:</span></b> Discussion list
for GROMACS
users<br>
<b><span style="font-weight: bold;">Subject:</span></b> Re:
[gmx-users] Troubles
with genbox and random insertion</span></font><font color="black"><span
style="color: windowtext;"><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;">Dear Shay,<br>
<br>
Use the -seed flag<br>
<br>
Ran.<br>
<br>
Shay Amram wrote: <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">Dear Gromacs users<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;"><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">I’m having a bit of a
trouble with genbox: I
want to insert 4 PLM (palmitate) molecules at random positions in my
simulation. <u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">So I tried running:<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; font-weight: bold; font-style: italic;">genbox
-cp cent_tim.gro -ci plm.gro -nmol 4 -o 4PLM_tim.gro -seed 100<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; font-weight: bold; font-style: italic;">pdb2gmx
-f 4PLM_tim.gro -o 4PLM_tim.gro -p –ter<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; font-weight: bold; font-style: italic;"><u1:p> </u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">I got a GRO file and
indeed there were 4 PLM
molecules. <u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><u><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">When I ran the same
script again, I
got the <b><span style="font-weight: bold;">exact</span></b> same GRO
file.</span></font></u><font face="Arial"><span
style="font-family: Arial;"> Meaning, the positioning of the PLM
molecules wasn’t truly random.<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;"><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">After reading the
Description on <u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;"><a
href="http://www.gromacs.org/documentation/reference/online/genbox.html">http://www.gromacs.org/documentation/reference/online/genbox.html</a><u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">I saw that the –ci flag
supposedly works only
if I insert one molecule.<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;"><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">So I tried a different
approach – to add a
single PLM four times like so:<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">#
Palmitate No.1<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">genbox
-cp cent_tim.gro -ci plm.gro -nmol 4 -o 1PLM_tim.gro<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">pdb2gmx
-f 1PLM_tim.gro -o 1PLM_tim.gro -p -ter<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;"><u1:p> </u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">#
Palmitate No.2<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">genbox
-cp 1PLM_tim.gro -ci plm.gro -nmol 1 -o 2PLM_tim.gro<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">pdb2gmx
-f 2PLM_tim.gro -o 2PLM_tim.gro -p -ter<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;"><u1:p> </u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">#
Palmitate No.3<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">genbox
-cp 2PLM_tim.gro -ci plm.gro -nmol 1 -o 3PLM_tim.gro<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">pdb2gmx
-f 3PLM_tim.gro -o 3PLM_tim.gro -p -ter<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;"><u1:p> </u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">#
Palmitate No.4<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">genbox
-cp 3PLM_tim.gro -ci plm.gro -nmol 1 -o 4PLM_tim.gro<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">pdb2gmx
-f 4PLM_tim.gro -o 4PLM_tim.gro -p –ter<u1:p></u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><b><i><font color="black" face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;"><u1:p> </u1:p></span></font></i></b><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">I got a different GRO
than the one I got when adding
the whole 4 of PLM in one line, <u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">but still, If I run the
same batch of commands again,
I get the same GRO file. <u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">If I run the first batch
50 times, each time
I’ll get the same GRO file as before. Same is true for the second
batch.
Meaning the positioning is not random.<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;"><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">I tried fiddling with it
some more (removing
“-seed 100” etc., ) and still the result is the same.<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;"><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">Thank you very much in
advance and best regards,<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">Shay Amram<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;"><br>
<br>
<br>
<o:p></o:p></span></font></p>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">-- <o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">------------------------------------------------------<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Ran Friedman<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Postdoctoral Fellow<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Computational Structural Biology Group (A. Caflisch)<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Department of Biochemistry<o:p></o:p></span></font></pre>
<pre><st1:place w:st="on"><st1:PlaceType w:st="on"><font color="black"
face="Courier New" size="2"><span style="font-size: 10pt;">University</span></font></st1:PlaceType> of <st1:PlaceName
w:st="on">Zurich</st1:PlaceName></st1:place><o:p></o:p></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Winterthurerstrasse 190<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">CH-8057 <st1:place w:st="on"><st1:City
w:st="on">Zurich</st1:City>, <st1:country-region w:st="on">Switzerland</st1:country-region></st1:place><o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Tel. +41-44-6355593<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Email: <a
href="mailto:r.friedman@bioc.unizh.ch">r.friedman@bioc.unizh.ch</a><o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Skype: ran.friedman<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">------------------------------------------------------<o:p></o:p></span></font></pre>
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</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
------------------------------------------------------
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