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<div class=Section1>
<p class=MsoNormal><span class=GramE><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Greetings all.</span></font></span><o:p></o:p></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'>I have a fatty acid monolayer system consisting of 64 <span
class=SpellE>arachidic</span> acid molecules in vacuum.<span
style='mso-spacerun:yes'> </span>We are trying to simulate a <span
class=SpellE>Langmuir</span> trough experiment in which the lateral pressure is
monitored as a function of the packing density.<span style='mso-spacerun:yes'>
</span>The x and y vectors of the box are initially set at values that provide
a monolayer packing density of 18.5 A^2/molecule.<span
style='mso-spacerun:yes'> </span><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'>At this packing density, I first perform a MD simulation for 1000 <span
class=SpellE>ps</span> with position restraints on all atoms.<span
style='mso-spacerun:yes'> </span>This is followed by another 1000 <span
class=SpellE>ps</span> simulation in which the acid <span class=SpellE>headgroups</span>
are position restrained while the aliphatic chains are not.<span
style='mso-spacerun:yes'> </span>I then execute a 2000 <span class=SpellE>ps</span>
simulation without restraints to allow equilibration followed by another 2000 <span
class=SpellE>ps</span> simulation for the analysis.<span
style='mso-spacerun:yes'> </span>Once this has been completed I take the
resulting <span class=SpellE>gromos</span> file and use <span class=SpellE>editconf</span>
to increase the box vectors so that a packing density of 19 A^2/molecule is
obtained.<span style='mso-spacerun:yes'> </span>Similar to the case of 18.5
A^2/molecule, a 2000 <span class=SpellE>ps</span> equilibration MD run is
completed for the 19 A^2/molecule system followed by another 2000 <span
class=SpellE>ps</span> simulation for analysis.<span style='mso-spacerun:yes'>
</span>The resulting <span class=SpellE>gromos</span> file from the second 2000
<span class=SpellE>ps</span> run for the 19 A^2/molecule system is then used
via <span class=SpellE>editconf</span> to generate a box size yielding a
packing density of 19.5 A^2/molecule.<span style='mso-spacerun:yes'>
</span>Again, a 2000 <span class=SpellE>ps</span> equilibration simulation is
conducted followed by a 2000 <span class=SpellE>ps</span> analysis run.<span
style='mso-spacerun:yes'> </span>This process is continued up to 25
A^2/molecule.<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'>As you probably expect, I am trying to generate a Pi-A (surface
pressure vs. area) isotherm by manipulating the area per molecule and
monitoring the pressure.<span style='mso-spacerun:yes'> </span>The problem I have
encountered is that the diagonal pressure values (Pres-XX, Pres-YY, and
Pres-ZZ) fluctuate quite drastically from one simulation at a given area per
molecule to another.<span style='mso-spacerun:yes'> </span>For example when
going from 18.5 to 19 A^2/molecule, I see an increase rather a decrease in the
diagonal pressure elements.<span style='mso-spacerun:yes'> </span>When going
from 19 to 19.5 A^2/molecule I observe a decrease in pressure followed by an
increase from 19.5 to 20 A^2/molecule.<span style='mso-spacerun:yes'>
</span>This occurs at all packing densities up to 25 A^2/molecule.<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'>The work described above, as noted, was performed in vacuum.<span
style='mso-spacerun:yes'> </span>There has been some work cited in the
literature in which an entire Pi-A diagram was obtained for a fatty acid
monolayer.<span style='mso-spacerun:yes'> </span>Their system was in vacuum,
however, they utilized a modified LJ potential in a plane just below the <span
class=SpellE>headgroups</span> to simulate the interaction of the fatty acids
with water (something my system is missing).<span style='mso-spacerun:yes'>
</span>Alternatively, I have also looked at work by <span class=SpellE>Alhstrom</span>
and <span class=SpellE>Berendsen</span> who simulated a lecithin monolayer
(using a dual monolayer system) and monitored the surface pressure at a
specified packing density which agreed quite well with experiments.<span
style='mso-spacerun:yes'> </span>They employed a dual monolayer system with a
layer of water in between the two <span class=SpellE>monolayers</span> (This
was done to provide periodic boundary conditions in z).<span
style='mso-spacerun:yes'> </span>I am in the process of conducting similar <span
class=GramE>simulations,</span> however, I first wanted to see if it is
possible to find any success with a system in vacuum.<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><span class=GramE><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Finally, to the question.</span></font></span><span
style='mso-spacerun:yes'> </span>Does anyone have any tips or suggestions?<span
style='mso-spacerun:yes'> </span>Below, I have provided some of the system
parameters in the event that anyone is interested.<span
style='mso-spacerun:yes'> </span>For example, I only generate velocities and
have a constrained start in the initial position restrained simulation.<span
style='mso-spacerun:yes'> </span>The length of the box in the z-direction is
7.5 nm (fatty acid length = 2.6 nm) so that the <span class=SpellE>headgroups</span>
do not interact with the chains.<span style='mso-spacerun:yes'> </span>The
methyl and <span class=SpellE>methylene</span> groups are represented by CH3
and CH2 groups in the GROMACS topology file.<span style='mso-spacerun:yes'>
</span>Periodic boundary conditions are imposed in xyz.<o:p></o:p></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'>Thank you,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Roger McMullen<o:p></o:p></span></font></p>
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