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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">Hi all<?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>I’m simulating membrane made of three types of
lipids.<SPAN style="mso-spacerun: yes"> </SPAN>I’m having problems with
longer runs.<SPAN style="mso-spacerun: yes"> </SPAN>After 600-900
<SPAN style="mso-spacerun: yes"> </SPAN>ps I always get large VCM.<SPAN
style="mso-spacerun: yes"> </SPAN>I checked lipid topology and it
seems ok.<SPAN style="mso-spacerun: yes"> </SPAN>Maybe there is some
problem with my *mdp file?<SPAN style="mso-spacerun: yes">
</SPAN>Please give me some comment on this, and thank you in
advance.</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>….</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman"><SPAN
style="mso-spacerun: yes">
</SPAN>Step<SPAN
style="mso-spacerun: yes">
</SPAN>Time<SPAN
style="mso-spacerun: yes">
</SPAN>Lambda<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman"><SPAN
style="mso-spacerun: yes">
</SPAN>305000<SPAN style="mso-spacerun: yes">
</SPAN>610.00000<SPAN
style="mso-spacerun: yes">
</SPAN>0.00000<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">
</SPAN>Rel. Constraint Deviation:<SPAN style="mso-spacerun: yes">
</SPAN>Max<SPAN style="mso-spacerun: yes"> </SPAN>between
atoms<SPAN style="mso-spacerun: yes">
</SPAN>RMS<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman"><SPAN
style="mso-spacerun: yes"> </SPAN>Before
LINCS<SPAN
style="mso-spacerun: yes">
</SPAN>0.072926<SPAN style="mso-spacerun: yes"> </SPAN>5163<SPAN
style="mso-spacerun: yes"> </SPAN>5166<SPAN
style="mso-spacerun: yes">
</SPAN>0.025714<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman"><SPAN
style="mso-spacerun: yes">
</SPAN>After LINCS<SPAN
style="mso-spacerun: yes">
</SPAN>0.000039<SPAN style="mso-spacerun: yes"> </SPAN>4759<SPAN
style="mso-spacerun: yes"> </SPAN>4760<SPAN
style="mso-spacerun: yes">
</SPAN>0.000009<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">
</SPAN>Energies (kJ/mol)<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT
face="Times New Roman"><SPAN lang=EN-US><SPAN
style="mso-spacerun: yes">
</SPAN>Bond<SPAN
style="mso-spacerun: yes">
</SPAN>Angle<SPAN style="mso-spacerun: yes"> </SPAN>Proper
Dih. Ryckaert-Bell.<SPAN style="mso-spacerun: yes"> </SPAN></SPAN><SPAN
lang=DE style="mso-ansi-language: DE">Improper
Dih.<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT face="Times New Roman"><SPAN
style="mso-spacerun: yes"> </SPAN>8.39732e+03<SPAN
style="mso-spacerun: yes"> </SPAN>1.67752e+04<SPAN
style="mso-spacerun: yes"> </SPAN>6.25326e+03<SPAN
style="mso-spacerun: yes"> </SPAN>3.60327e+03<SPAN
style="mso-spacerun: yes">
</SPAN>8.99070e+02<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT
face="Times New Roman"><SPAN lang=DE style="mso-ansi-language: DE"><SPAN
style="mso-spacerun: yes">
</SPAN></SPAN><SPAN lang=EN-US>LJ-14<SPAN
style="mso-spacerun: yes"> </SPAN>Coulomb-14<SPAN
style="mso-spacerun: yes"> </SPAN>LJ
(SR)<SPAN style="mso-spacerun: yes"> </SPAN>Coulomb (SR)<SPAN
style="mso-spacerun: yes">
</SPAN>Potential<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT
face="Times New Roman"><SPAN lang=EN-US><SPAN
style="mso-spacerun: yes"> </SPAN></SPAN><SPAN lang=DE
style="mso-ansi-language: DE">9.39095e+03<SPAN
style="mso-spacerun: yes"> </SPAN>-1.99649e+04<SPAN
style="mso-spacerun: yes"> </SPAN>1.75564e+04<SPAN
style="mso-spacerun: yes"> </SPAN>-4.71882e+05<SPAN
style="mso-spacerun: yes">
</SPAN>-4.28971e+05<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT
face="Times New Roman"><SPAN lang=DE style="mso-ansi-language: DE"><SPAN
style="mso-spacerun: yes"> </SPAN>Kinetic En.<SPAN
style="mso-spacerun: yes"> </SPAN></SPAN><SPAN lang=EN-US>Total
Energy<SPAN style="mso-spacerun: yes"> </SPAN>Temperature
Pressure (bar)<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT
face="Times New Roman"><SPAN lang=EN-US><SPAN
style="mso-spacerun: yes"> </SPAN></SPAN><SPAN lang=DE
style="mso-ansi-language: DE">7.62203e+04<SPAN
style="mso-spacerun: yes"> </SPAN>-3.52751e+05<SPAN
style="mso-spacerun: yes"> </SPAN>3.02711e+02<SPAN
style="mso-spacerun: yes">
</SPAN>-6.42276e+02<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><o:p><FONT face="Times New Roman"
size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT face="Times New Roman">Large
VCM(group PC):<SPAN style="mso-spacerun: yes">
</SPAN>237.90714,<SPAN style="mso-spacerun: yes"> </SPAN>-2554.62744,<SPAN
style="mso-spacerun: yes"> </SPAN>2074.48413, ekin-cm:<SPAN
style="mso-spacerun: yes">
</SPAN>2.90949e+11<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">Large VCM(group SOL):<SPAN
style="mso-spacerun: yes"> </SPAN>-110.55383,<SPAN
style="mso-spacerun: yes"> </SPAN>1187.11670,<SPAN
style="mso-spacerun: yes"> </SPAN>-964.00018, ekin-cm:<SPAN
style="mso-spacerun: yes">
</SPAN>1.35202e+11<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">There were 2 inconsistent shifts. Check your
topology<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">Large VCM(group PC): -144534.25000,
1364136.62500, -1206019.87500, ekin-cm:<SPAN style="mso-spacerun: yes">
</SPAN>8.91658e+16<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">Large VCM(group SOL): -23919.93359,
-1180828.00000, -975466.56250, ekin-cm:<SPAN style="mso-spacerun: yes">
</SPAN>1.34954e+17<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>Large VCM(group PC):<SPAN
style="mso-spacerun: yes">
</SPAN>inf,<SPAN
style="mso-spacerun: yes">
</SPAN>-inf,<SPAN
style="mso-spacerun: yes">
</SPAN>inf, ekin-cm:<SPAN
style="mso-spacerun: yes"> </SPAN><SPAN
style="mso-spacerun: yes"> </SPAN>inf</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman"
size=3>-------------------------------------------------------------------------</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">My mdp:<SPAN
style="mso-spacerun: yes"> </SPAN></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">;<SPAN
style="mso-spacerun: yes"> </SPAN>User spoel
(236)<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT
face="Times New Roman"><SPAN lang=EN-US>;<SPAN
style="mso-spacerun: yes"> </SPAN>Wed
Nov<SPAN style="mso-spacerun: yes"> </SPAN>3 </SPAN><?xml:namespace prefix
= st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:time Hour="17"
Minute="12"><SPAN lang=EN-US>17:12:44</SPAN></st1:time><SPAN lang=EN-US>
1993<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">;<SPAN
style="mso-spacerun: yes"> </SPAN>Input
file<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">;<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">title<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>4ns ps pe
pc<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">cpp<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>/lib/cpp<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">define<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>-DFLEX_SPC<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">constraints<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>h-bonds<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">integrator<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>md<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">dt<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>0.002<SPAN
style="mso-spacerun: yes"> </SPAN>; ps
!<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">nsteps<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>2000000<SPAN
style="mso-spacerun: yes"> </SPAN>; total 1000
ps.<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">nstxout<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>50000<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">nstvout<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>50000<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">nstfout<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>50000<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT
face="Times New Roman">nstlog<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>5000<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT
face="Times New Roman">nstenergy<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>1000<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT
face="Times New Roman">nstlist<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>10<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT
face="Times New Roman">ns_type<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>grid<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">rlist<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>1.0<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">; Method for doing
VdW<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">vdw-type<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>Cut-off<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">rvdw<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>1.0<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">; Method for doing
electrostatics<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">coulombtype<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>PME<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">rcoulomb<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>1<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">fourierspacing<SPAN
style="mso-spacerun: yes"> </SPAN>=<SPAN
style="mso-spacerun: yes"> </SPAN>0.12<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">fourier_nx<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>0<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">fourier_ny<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>0<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">fourier_nz<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>0<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">pme_order<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>4<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">ewald_rtol<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>1e-5<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">optimize_fft<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>yes<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">; Berendsen temperature coupling is on in
two groups<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">Tcoupl<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>berendsen<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">tc-grps<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>PC<SPAN
style="mso-spacerun: yes"> </SPAN>PE PS<SPAN
style="mso-spacerun: yes"> </SPAN>SOL
Na<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT
face="Times New Roman">tau_t<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>0.1<SPAN
style="mso-spacerun: yes"> </SPAN>0.1<SPAN
style="mso-spacerun: yes"> </SPAN>0.1<SPAN
style="mso-spacerun: yes"> </SPAN>0.1
0.1<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT
face="Times New Roman">ref_t<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>310 310 310 310
310<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT face="Times New Roman">; Energy
monitoring<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">energygrps<SPAN
style="mso-spacerun: yes">
</SPAN>= PC<SPAN style="mso-spacerun: yes"> </SPAN>PE PS<SPAN
style="mso-spacerun: yes"> </SPAN>SOL
Na<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">; Isotropic pressure coupling is now
on<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">Pcoupl<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>berendsen<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">Pcoupltype<SPAN
style="mso-spacerun: yes">
</SPAN>= semiisotropic<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">tau_p<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>20<SPAN
style="mso-spacerun: yes">
</SPAN>20<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">compressibility<SPAN
style="mso-spacerun: yes"> </SPAN>=<SPAN
style="mso-spacerun: yes"> </SPAN>4.5e-5<SPAN
style="mso-spacerun: yes">
</SPAN>4.5e-5<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">ref_p<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>1.0<SPAN
style="mso-spacerun: yes"> </SPAN>1.0<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">; Generate velocites is off at 300
K.<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT
face="Times New Roman">gen_vel<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>yes<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT
face="Times New Roman">gen_temp<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>310.0<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE
style="mso-ansi-language: DE"><FONT size=3><FONT
face="Times New Roman">gen_seed<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>173529<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">; Groups for center of mass motion
removal<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">comm-grps<SPAN
style="mso-spacerun: yes">
</SPAN>= PC<SPAN style="mso-spacerun: yes"> </SPAN>PE PS<SPAN
style="mso-spacerun: yes"> </SPAN>SOL
Na<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">; Mode for center of mass motion
removal<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">comm-mode<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>Linear<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">; Center of mass
control<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">nstcomm<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>1<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">; Periodic boundary
conditions<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">pbc<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>xyz<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><SPAN
style="mso-spacerun: yes"><FONT face="Times New Roman"
size=3>
</FONT></SPAN></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman"
size=3> </FONT></o:p></SPAN></P></FONT></DIV></BODY></HTML>