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Dear Shay,<br>
<br>
Use the -seed flag<br>
<br>
Ran.<br>
<br>
Shay Amram wrote:
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<p class="MsoNormal"><font face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">Dear Gromacs users<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font 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. <o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">So I tried running:<o:p></o:p></span></font></p>
<p class="MsoNormal"><b><i><font 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<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font 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<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; font-weight: bold; font-style: italic;"><o:p> </o:p></span></font></i></b></p>
<p class="MsoNormal"><font face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">I got a GRO file and
indeed there were 4 PLM molecules. <o:p></o:p></span></font></p>
<p class="MsoNormal"><u><font 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.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">After reading the
Description on <o:p></o:p></span></font></p>
<p class="MsoNormal"><font 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><o:p></o:p></span></font></p>
<p class="MsoNormal"><font 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.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font 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:<o:p></o:p></span></font></p>
<p class="MsoNormal"><b><i><font face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">#
Palmitate No.1<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font 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<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font 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<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;"><o:p> </o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">#
Palmitate No.2<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font 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<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font 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<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;"><o:p> </o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">#
Palmitate No.3<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font 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<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font 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<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;"><o:p> </o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;">#
Palmitate No.4<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font 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<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font 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<o:p></o:p></span></font></i></b></p>
<p class="MsoNormal"><b><i><font face="Arial" size="1"><span
style="font-size: 8pt; font-family: Arial; font-weight: bold; font-style: italic;"><o:p> </o:p></span></font></i></b></p>
<p class="MsoNormal"><font 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, <o:p></o:p></span></font></p>
<p class="MsoNormal"><font 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. <o:p></o:p></span></font></p>
<p class="MsoNormal"><font 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.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font 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.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">Thank you very much in
advance and best regards,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="3"><span
style="font-size: 12pt; font-family: Arial;">Shay Amram<o:p></o:p></span></font></p>
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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
------------------------------------------------------
</pre>
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