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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dear all,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I want to make an ideal semipermeable membrane comprised of
several hundreds of atom CM in a plane, which is fully permeable to water but
resistant to NaCl. I defined atomtype CM (CM is neutral)<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>[ atomtypes ]<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'> CM 6
12.01 0.000 A
2.22343e-03 3.434770e-06<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>In order to turn off the LJ interaction between CM and H2O,
I specified<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>[ nonbond_params ]<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>; i j
func
c6 c12<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span lang=DE
style='font-size:10.0pt;font-family:"Courier New"'>
OW CM 1 0.0000000e-03 0.00000e-06<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=DE style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>After I make a system (SOL phase + semipermeable membrane +
NaCl phase), I run energy minimization. But after EM, I found there is an
obvious space between SOL phase (or NaCl phase) and membrane. In the initial
structure, this pace does not exist. So it means that this membrane still has
LJ interaction with SOL. I also use g_energy command to check the LJ_SR
interaction between membrane and SOL, the obtained LJ_SR interaction energy is not
equal to zero.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Why do membrane and SOL still have LJ interaction when I
turn off it in my topology file? What is the correct step to turn off LJ
interaction between two groups?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=DE style='font-size:10.0pt;
font-family:Arial'>Best wishes,</span></font><span lang=DE><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=DE style='font-size:10.0pt;
font-family:Arial'>Zhongqiao<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=DE style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dept of Chem & Biomole Engin<o:p></o:p></span></font></p>
<p class=MsoNormal><st1:PlaceName w:st="on"><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>National</span></font></st1:PlaceName><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> <st1:PlaceType
w:st="on">University</st1:PlaceType> of <st1:country-region w:st="on"><st1:place
w:st="on">Singapore</st1:place></st1:country-region><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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