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<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Dear Gromacs users<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 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. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>So I tried running:<o:p></o:p></span></font></p>
<p class=MsoNormal><b><i><font size=2 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<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 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<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'><o:p> </o:p></span></font></i></b></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
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 size=3 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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>After reading the Description on <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 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><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 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:<o:p></o:p></span></font></p>
<p class=MsoNormal><b><i><font size=1 face=Arial><span style='font-size:8.0pt;
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 size=1 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<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=1 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<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=1 face=Arial><span style='font-size:8.0pt;
font-family:Arial;font-weight:bold;font-style:italic'><o:p> </o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=1 face=Arial><span style='font-size:8.0pt;
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 size=1 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<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=1 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<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=1 face=Arial><span style='font-size:8.0pt;
font-family:Arial;font-weight:bold;font-style:italic'><o:p> </o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=1 face=Arial><span style='font-size:8.0pt;
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 size=1 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<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=1 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<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=1 face=Arial><span style='font-size:8.0pt;
font-family:Arial;font-weight:bold;font-style:italic'><o:p> </o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=1 face=Arial><span style='font-size:8.0pt;
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 size=1 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<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=1 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<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=1 face=Arial><span style='font-size:8.0pt;
font-family:Arial;font-weight:bold;font-style:italic'><o:p> </o:p></span></font></i></b></p>
<p class=MsoNormal><font size=3 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, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 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. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Thank you very much in advance and best regards,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Shay Amram<o:p></o:p></span></font></p>
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