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<title> Hi all, I am trying to simulate a lipid bilayer (at plain XY, such
that it is normal to Z) with water at the two sides</title>
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<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'><span style='mso-spacerun:yes'> </span>Hi all, I am
trying to simulate a lipid <span class=SpellE>bilayer</span> (at plain XY, such
that it is normal to Z) with water at the two sides.<span
style='mso-spacerun:yes'> </span>When I do PR dynamics, using:<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"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>title</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>DMPC bi-layer solvated in water and Na ions.<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cpp</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>/<span class=SpellE>usr/bin/cpp</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>integrator</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span><span class=SpellE>md</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>dt</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>0.002<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>nsteps</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>50000<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>;
Constrain control<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>define</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>= -DPOSRES<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>constraints</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>= all-bonds<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>;
Output frequency for <span class=SpellE>coords</span> (x), velocities (v) and
forces (f)<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>nstxout</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'> </span>500<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>nstvout</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>500<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>nstfout</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>500<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>;
<span class=SpellE><span class=GramE>nblist</span></span> update frequency<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>nstlist</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>10 <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>;
<span class=GramE>ns</span> algorithm <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>ns_type</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>grid</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>rlist</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span
style='mso-spacerun:yes'> </span>1.3<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>coulombtype</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-tab-count:1'> </span><span style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>PME<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>rcoulomb</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>1.3<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>rvdw</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>1.3<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>fourierspacing</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-tab-count:1'> </span><span style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>0.10<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>fourier_nx</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-tab-count:1'> </span><span style='mso-spacerun:yes'> </span><span
class=GramE>=<span style='mso-spacerun:yes'> </span>0</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>fourier_ny</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-tab-count:1'> </span><span style='mso-spacerun:yes'> </span><span
class=GramE>=<span style='mso-spacerun:yes'> </span>0</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>fourier_nz</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-tab-count:1'> </span><span style='mso-spacerun:yes'> </span><span
class=GramE>=<span style='mso-spacerun:yes'> </span>0</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>pme_order</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-tab-count:1'> </span><span style='mso-spacerun:yes'> </span><span
class=GramE>=<span style='mso-spacerun:yes'> </span>6</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>ewald_rtol</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-tab-count:1'> </span><span style='mso-spacerun:yes'> </span><span
class=GramE>=<span style='mso-spacerun:yes'> </span>1e</span>-5<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>optimize_fft</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>yes</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>;
<span class=SpellE>Berendsen</span> temperature coupling is on in three groups<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>Tcoupl</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span><span class=SpellE>berendsen</span></span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>tau_t</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>0.1</span><span
style='mso-spacerun:yes'> </span><span class=SpellE>0.1</span><span
style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>tc-grps</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-tab-count:2'> </span><span style='mso-spacerun:yes'>
</span>=<span style='mso-spacerun:yes'> </span>Solvent<span
style='mso-spacerun:yes'> </span>DMPC<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>ref_t</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>310</span><span
style='mso-spacerun:yes'> </span><span class=SpellE>310</span> <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>;
Pressure coupling is on<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>Pcoupl</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span><span class=SpellE>berendsen</span></span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>pcoupltype</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span><span class=SpellE>semiisotropic</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>tau_p</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>2</span> <span class=SpellE>2</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>compressibility</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>4.5e-5 0<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>ref_p</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>1.0</span> <span class=SpellE>1.0</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>;
Generate <span class=SpellE>velocites</span> is on at 310 K.<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>gen_vel</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>yes</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>gen_temp</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span><span class=GramE>=<span
style='mso-spacerun:yes'> </span>310</span><o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>;
Electric field - used<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>;
100mV/3nm*10E-3v/mV = 0.033<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'>E_z</span></font></span><font size=2
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'> = <span
class=GramE>1<span style='mso-spacerun:yes'> </span>0.033</span><span
style='mso-spacerun:yes'> </span>0.0<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>;
Energy monitoring<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>energygrps</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>SOL DMPC<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>;
Center of mass control<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>nstcomm</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>1<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>comm-grps</span></font></span></span><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><span
style='mso-spacerun:yes'> </span>=<span style='mso-spacerun:yes'>
</span>Solvent<span style='mso-spacerun:yes'> </span>DMPC<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'><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"'>I got from the <span class=SpellE>mdrun</span> a box
with different size then the one entered.<span style='mso-spacerun:yes'>
</span>I know I used pressure coupling, which might change the box, but the <span
class=SpellE>bilayer</span> is ruined. I saw in articles (e.g. <span
class=SpellE>Biophys</span> J. 2002 Jun<span class=GramE>;82</span>(6):2934-42.)
that</span></font><font size=2><span style='font-size:10.0pt'> </span></font><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>it
is possible to allow changes only at the z axis, how this is done?<span
style='mso-spacerun:yes'> </span>Does working this way, will keep the <span
class=SpellE>bilayer</span> and it’s properties physically?<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"'><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"'><span style='mso-spacerun:yes'> </span>And a second
question if I may, when running <span class=SpellE>gromacs</span>, is it better
to give to any CPU more then one job.<span style='mso-spacerun:yes'> </span>For
instance, if I have two CPU is it more efficient to cut the job into four
parallel processes?<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"'><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"'><span style='mso-spacerun:yes'> </span>Thanks
you all, Itamar.<o:p></o:p></span></font></p>
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