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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Two ways:<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:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>1 – turn them off with the visualisation software you are using,
only display the protein and lipid<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>2 – use editconf and the appropriate index groups<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;color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
Department of Pharmaceutical Biology and Pharmacology<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='color:#1F497D'> </span><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p>
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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>nitu sharma<br>
<b>Sent:</b> Thursday, 11 June 2009 3:19 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] problem regarding removal of water from final
simulation system.<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Dear all <br>
<br>
I have done successfully simulation of membrane protein , but after that
to visualise my final model clearly I have to remove water molecules from my
system (protein+lipid+water).<br>
<br>
But I have no Idea about the which command I should use to do this even
it doesn't mentioned in justin,s tutorial also to make final pdb after
simulation.<br>
<br>
So can anyone suggest me how to remove water form my final simulation
system to make final pdb of only protein and lipid molecule?<br>
<br>
If anyone can help me I willbe really thankful for him/her.<br>
<br>
Nitu Sharma.<br>
Jawaherlal Nehru University<br>
New Delhi , India.<o:p></o:p></p>
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