That's the whole idea, you _have_ to change the seed value, since it's used by the program to generate a sequence of pseudorandom numbers...<br><br><div><span class="gmail_quote">2007/9/18, Shay Amram <<a href="mailto:shayamra@post.tau.ac.il">
shayamra@post.tau.ac.il</a>>:</span><blockquote class="gmail_quote" style="margin-top: 0; margin-right: 0; margin-bottom: 0; margin-left: 0; margin-left: 0.80ex; border-left-color: #cccccc; border-left-width: 1px; border-left-style: solid; padding-left: 1ex">
<div bgcolor="#ffffff" lang="EN-US" link="#0000ff" vlink="#800080"><div><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial; color: WindowText">Greetings Ran,</span></font></p><p>
<font size="3" color="#000000" face="Arial"><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.
</span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial">(ran the following command:)</span></font></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">
genbox -cp cent_tim.gro -ci plm.gro -nmol 4 -o 1PLM_tim.gro –seed 4</span></font></i></b></p><p><font size="3" color="#000000" face="Times New Roman"><span style="font-size: 12pt"> </span></font></p><p><font size="3" color="#000000" face="Times New Roman">
<span style="font-size: 12pt">Each time I change the number after "-seed" I get a different GRO file,</span></font></p><p><font size="3" color="#000000" face="Times New Roman"><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.
</span></font></p><p><font size="3" color="#000000" face="Times New Roman"><span style="font-size: 12pt"> </span></font></p><p><font size="3" color="#000000" face="Times New Roman"><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?
</span></font></p><p><font size="3" color="#000000" face="Times New Roman"><span style="font-size: 12pt"> </span></font></p><p><font size="3" color="#000000" face="Times New Roman"><span style="font-size: 12pt">Thanks,</span>
</font></p><p><font size="3" color="#000000" face="Times New Roman"><span style="font-size: 12pt">-Shay</span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial; color: WindowText">
</span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial; color: WindowText"> </span></font></p><div><div align="center" style="text-align: center"><font size="3" color="#000000" face="Times New Roman">
<span style="font-size: 12pt; color: WindowText"><hr size="2" width="100%" align="center"></span></font></div><p><b><font size="2" color="#000000" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; color: WindowText; font-weight: 700">
From:</span></font></b><font size="2" color="#000000" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; color: WindowText"> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-bounces@gromacs.org</a>] <b><span style="font-weight: 700">
On Behalf Of </span></b>Ran Friedman<br><b><span style="font-weight: 700">Sent:</span></b> Tuesday, September 18, 2007 14:40<br><b><span style="font-weight: 700">To:</span></b> Discussion list for GROMACS users<br><b><span style="font-weight: 700">
Subject:</span></b> Re: [gmx-users] Troubles with genbox and random insertion</span></font></p></div><div><span class="e" id="q_11518ca985fb375d_1"><p><font size="3" color="#000000" face="Times New Roman"><span style="font-size: 12pt">
</span></font></p><p><font size="3" color="#000000" face="Times New Roman"><span style="font-size: 12pt">Dear Shay,<br><br> Use the -seed flag<br><br> Ran.<br><br> Shay Amram wrote: </span></font></p><p><font size="3" color="#000000" face="Arial">
<span style="font-size: 12pt; font-family: Arial">Dear Gromacs users</span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial"> </span></font></p><p><font size="3" color="#000000" face="Arial">
<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. </span></font></p><p><font size="3" color="#000000" face="Arial">
<span style="font-size: 12pt; font-family: Arial">So I tried running:</span></font></p><p><b><i><font size="2" color="#000000" face="Arial"><span style="font-size: 10pt; font-family: Arial; font-weight: 700; font-style: italic">
genbox -cp cent_tim.gro -ci plm.gro -nmol 4 -o 4PLM_tim.gro -seed 100</span></font></i></b></p><p><b><i><font size="2" color="#000000" face="Arial"><span style="font-size: 10pt; font-family: Arial; font-weight: 700; font-style: italic">
pdb2gmx -f 4PLM_tim.gro -o 4PLM_tim.gro -p –ter</span></font></i></b></p><p><b><i><font size="2" color="#000000" face="Arial"><span style="font-size: 10pt; font-family: Arial; font-weight: 700; font-style: italic"> </span>
</font></i></b></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial">I got a GRO file and indeed there were 4 PLM molecules. </span></font></p><p><u><font size="3" color="#000000" face="Arial">
<span style="font-size: 12pt; font-family: Arial">When I ran the same script again, I got the <b><span style="font-weight: 700">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.</span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial"> </span></font></p><p><font size="3" color="#000000" face="Arial">
<span style="font-size: 12pt; font-family: Arial">After reading the Description on </span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial"><a href="http://www.gromacs.org/documentation/reference/online/genbox.html" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://www.gromacs.org/documentation/reference/online/genbox.html</a></span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial">I saw that the –ci flag supposedly works only if I insert one molecule.
</span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial"> </span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial">
So I tried a different approach – to add a single PLM four times like so:</span></font></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">
# Palmitate No.1</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">genbox -cp cent_tim.gro -ci plm.gro -nmol 4 -o 1PLM_tim.gro
</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">pdb2gmx -f 1PLM_tim.gro -o 1PLM_tim.gro -p -ter</span></font>
</i></b></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic"> </span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial">
<span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic"># Palmitate No.2</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">
genbox -cp 1PLM_tim.gro -ci plm.gro -nmol 1 -o 2PLM_tim.gro</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">
pdb2gmx -f 2PLM_tim.gro -o 2PLM_tim.gro -p -ter</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic"> </span>
</font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic"># Palmitate No.3</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial">
<span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">genbox -cp 2PLM_tim.gro -ci plm.gro -nmol 1 -o 3PLM_tim.gro</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial">
<span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">pdb2gmx -f 3PLM_tim.gro -o 3PLM_tim.gro -p -ter</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">
</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic"># Palmitate No.4</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial">
<span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">genbox -cp 3PLM_tim.gro -ci plm.gro -nmol 1 -o 4PLM_tim.gro</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial">
<span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">pdb2gmx -f 4PLM_tim.gro -o 4PLM_tim.gro -p –ter</span></font></i></b></p><p><b><i><font size="1" color="#000000" face="Arial"><span style="font-size: 8pt; font-family: Arial; font-weight: 700; font-style: italic">
</span></font></i></b></p><p><font size="3" color="#000000" face="Arial"><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, </span></font>
</p><p><font size="3" color="#000000" face="Arial"><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. </span></font></p><p><font size="3" color="#000000" face="Arial">
<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.</span></font>
</p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial"> </span></font></p><p><font size="3" color="#000000" face="Arial"><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.
</span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial"> </span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial">
Thank you very much in advance and best regards,</span></font></p><p><font size="3" color="#000000" face="Arial"><span style="font-size: 12pt; font-family: Arial">Shay Amram</span></font></p><p><font size="3" color="#000000" face="Times New Roman">
<span style="font-size: 12pt"><br><br><br></span></font></p><pre><font size="2" color="#000000" face="Courier New"><span style="font-size: 10pt">-- </span></font></pre><pre><font size="2" color="#000000" face="Courier New">
<span style="font-size: 10pt">------------------------------------------------------</span></font></pre><pre><font size="2" color="#000000" face="Courier New"><span style="font-size: 10pt">Ran Friedman</span></font></pre>
<pre><font size="2" color="#000000" face="Courier New"><span style="font-size: 10pt">Postdoctoral Fellow</span></font></pre><pre><font size="2" color="#000000" face="Courier New"><span style="font-size: 10pt">Computational Structural Biology Group (A. Caflisch)
</span></font></pre><pre><font size="2" color="#000000" face="Courier New"><span style="font-size: 10pt">Department of Biochemistry</span></font></pre><pre><font size="2" color="#000000" face="Courier New"><span style="font-size: 10pt">
University</span></font> of Zurich</pre><pre><font size="2" color="#000000" face="Courier New"><span style="font-size: 10pt">Winterthurerstrasse 190</span></font></pre><pre><font size="2" color="#000000" face="Courier New">
<span style="font-size: 10pt">CH-8057 Zurich, Switzerland</span></font></pre><pre><font size="2" color="#000000" face="Courier New"><span style="font-size: 10pt">Tel. +41-44-6355593</span></font></pre><pre><font size="2" color="#000000" face="Courier New">
<span style="font-size: 10pt">Email: <a href="mailto:r.friedman@bioc.unizh.ch" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">r.friedman@bioc.unizh.ch</a></span></font></pre><pre><font size="2" color="#000000" face="Courier New">
<span style="font-size: 10pt">Skype: ran.friedman</span></font></pre><pre><font size="2" color="#000000" face="Courier New"><span style="font-size: 10pt">------------------------------------------------------</span></font>
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