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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>How are you visualizing the system? Using VMD? In that case,
bonds are determined by how far apart the atoms are, it guesses what the
bonding is, since a .gro file (or a pdb) doesn’t have any bonding information
in it. So what you are seeing is simply the fact you have scaled the box,
increasing or decreasing the distance between the atoms. After a quick EM the
atoms will return to their correct spacing.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
Department of Pharmaceutical Biology <br>
Pharmacy and Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@pharm.monash.edu.au<br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>DreamCatcher<br>
<b>Sent:</b> Wednesday, 28 October 2009 1:50 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] some prolem about genbox genconf and editconf<o:p></o:p></span></p>
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<p class=MsoNormal>Hi everybody,<o:p></o:p></p>
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<p class=MsoNormal> I have come across some problem when
using genbox, genconf and editconf try to make a box with a certain density and
a certain number of polymer chains.<o:p></o:p></p>
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<p class=MsoNormal>First, I use genbox to have one polymer chain filled in the
box without any solvent.Then I use genconf to pile up 27 polymer chains ,after
that I use editconf to designate a density of 0.3 g/ml to attain the
final goal. When I finish it, i find that all the bond that connect the atoms
are gone and all the atoms disperse in the box.<o:p></o:p></p>
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<p class=MsoNormal> In another try, I first use a pdb file which
contains only one polymer chain to genconf a box with 27polymer chain, and then
use editconf to designate the density, but finally I get a box with lots of
bonds that might not present in a normal structure, like a carbon was bonded
with a 3 or 4 or even more atoms distance long and the bonds connect with it is
overcount. What is the prolem? How can I fix it? <o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Thanks in advance,<o:p></o:p></p>
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<p class=MsoNormal>Celeste<o:p></o:p></p>
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