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<p class=MsoNormal><font size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:windowtext'>Greetings Ran,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face=Arial><span style='font-size:
12.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial'>(ran the following command:)<o:p></o:p></span></font></p>
<p class=MsoNormal><b><i><font size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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 size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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 size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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 size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>Thanks,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>-Shay<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:windowtext'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial;color:windowtext'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
color=black face="Times New Roman"><span style='font-size:12.0pt;color:windowtext'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 color=black face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma;color:windowtext;font-weight:bold'>From:</span></font></b><font
size=2 color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:windowtext'> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <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 size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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 size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial'>Dear Gromacs users<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face=Arial><span style='font-size:
12.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial'>So I tried running:<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><b><i><font size=2 color=black face=Arial><span
style='font-size:10.0pt;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 size=2 color=black face=Arial><span
style='font-size:10.0pt;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 size=2 color=black face=Arial><span
style='font-size:10.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;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 size=3 color=black face=Arial><span
style='font-size:12.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial'>After reading the Description on <u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face=Arial><span style='font-size:
12.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face=Arial><span style='font-size:
12.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=1 color=black face=Arial><span
style='font-size:8.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face=Arial><span style='font-size:
12.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face=Arial><span style='font-size:
12.0pt;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 size=3 color=black face=Arial><span style='font-size:
12.0pt;font-family:Arial'>Shay Amram<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'><br>
<br>
<br>
<o:p></o:p></span></font></p>
<pre><font size=2 color=black face="Courier New"><span style='font-size:10.0pt'>-- <o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>------------------------------------------------------<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Ran Friedman<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Postdoctoral Fellow<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Computational Structural Biology Group (A. Caflisch)<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Department of Biochemistry<o:p></o:p></span></font></pre><pre><st1:place
w:st="on"><st1:PlaceType w:st="on"><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>University</span></font></st1:PlaceType> of <st1:PlaceName
w:st="on">Zurich</st1:PlaceName></st1:place><o:p></o:p></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Winterthurerstrasse 190<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>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
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Tel. +41-44-6355593<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Email: <a
href="mailto:r.friedman@bioc.unizh.ch">r.friedman@bioc.unizh.ch</a><o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Skype: ran.friedman<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>------------------------------------------------------<o:p></o:p></span></font></pre></div>
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