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<p class=MsoNormal><span style='color:#1F497D'>Why is it that what you have run
with xy rigid and z couple not correct? Fluctuating box volume is exactly what
you would expect to get, and do get, with pressure coupling.<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
</span><span style='font-size:10.0pt;color:#1F497D'>Drug Delivery, Disposition
and Dynamics</span><span style='font-size:10.0pt;color:#1F497D'><br>
</span><span style='font-size:10.0pt;color:#1F497D'>Monash Institute of
Pharmaceutical Sciences</span><span style='font-size:10.0pt;color:#1F497D'>,
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'> <o:p></o:p></span></p>
</div>
<p class=MsoNormal><span style='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>Matteus Lindgren<br>
<b>Sent:</b> Friday, 26 February 2010 8:24 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Anisotropic pressure control<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span lang=SV>Dear experts,<o:p></o:p></span></p>
<p class=MsoNormal><span lang=SV><o:p> </o:p></span></p>
<p class=MsoNormal>I am trying to run MD on a protein in water above a flat
surface of TiO2 in a cubic box with pressure control. All the atoms of TiO2 are
frozen and I therefore think that anisotropic pressure control must be used. I
tried allowing box fluctuations in the direction of the normal vector (the
z-axis) of the TiO2 surface but the box volume then oscillates during the whole
simulation. The same parameters worked for a simulation of protein+water without
the frozen TiO2 surface. <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>How can I use pressure control for a system with a frozen
surface that extends through the whole box? Ive read the posts about membrane
simulations but membranes are flexible so I think those suggestions might not
apply. <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>The important part of the input file was as follows:<o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><span lang=SV style='font-size:
10.0pt;font-family:"Courier New"'>nstlist
= 10<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=SV style='font-size:
10.0pt;font-family:"Courier New"'>ns_type
= grid<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=SV style='font-size:
10.0pt;font-family:"Courier New"'>pbc
= xyz<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=SV style='font-size:
10.0pt;font-family:"Courier New"'>periodic_molecules
= no<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>rlist
= 1.2<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>coulombtype
= PME<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>rcoulomb-switch
= 0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>rcoulomb
= 1.2<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>epsilon-r
= 1<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>epsilon_rf
= 1<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>vdw-type
= Cut-off<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>rvdw-switch
= 0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>rvdw
= 1.4<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>DispCorr
= EnerPres<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>table-extension
= 1.5<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>energygrp_table
= <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>fourierspacing
= 0.12<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>pme_order
= 4<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>ewald_rtol
= 1e-05<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>ewald_geometry
= 3d<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>optimize_fft
= yes<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>Tcoupl
= Nose-hoover<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=SV style='font-size:
10.0pt;font-family:"Courier New"'>tc-grps
= protres RUT solcl<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=SV style='font-size:
10.0pt;font-family:"Courier New"'>tau_t
= 0.1 0.1 0.1 <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>ref_t
= 310 310 310 <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>Pcoupl
= Parrinello-Rahman<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>Pcoupltype
= anisotropic<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>tau_p
= 2.0 2.0 2.0 2.0 2.0 2.0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>compressibility
= 0.0 0.0 5e-5 0.0 0.0 0.0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>ref_p
= 0 0 1.01325 0 0 0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=SV style='font-size:
10.0pt;font-family:"Courier New"'>gen_vel
= yes<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=SV style='font-size:
10.0pt;font-family:"Courier New"'>gen_temp
= 310<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>gen_seed
= 1993<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>constraints
= hbonds<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>constraint-algorithm = lincs<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>continuation
= yes<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>lincs-order
= 4<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>lincs-iter
= 4<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=SV style='font-size:
10.0pt;font-family:"Courier New"'>freezegrps
= frozen<o:p></o:p></span></p>
<p class=MsoNormal><span lang=SV style='font-size:10.0pt;font-family:"Courier New"'>freezedim
= Y Y Y</span><o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks<o:p></o:p></p>
<p class=MsoNormal>Matteus<o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>--------------------------------------------------------- <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Matteus
Lindgren, graduate student<br>
Department of Chemistry, Umeå University <br>
SE-901 87 Umeå, Sweden<br>
Phone: +46 (0)90-7865368 <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'> <o:p></o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
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