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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Plot the fluctuations of the pressure with time for the
simulation. Far better way I think to get an idea of what is going on with a
property than just looking at values in a log file. Especially when you are
starting out.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>With pressure coupling, it is not unusual to have a fluctuation
of a hundred or so. And that is nothing to worry about, entirely normal
behaviour to observe. And with such large fluctuations, the average pressure can
deviate from the reference pressure. Of course, with more sample points and
longer simulation time, it will get closer to the reference value.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
Department of Pharmaceutical Biology <br>
Pharmacy and Pharmaceutical Sciences, 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='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
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>Pan Wu<br>
<b>Sent:</b> Monday, 12 October 2009 2:20 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Pressure problem: pressure is too large during
MDsimulation<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi gmx users,<o:p></o:p></p>
<div>
<p class=MsoNormal> I am now simulating one protein with
solvent, in all atom forcefield, gromacs official distributed version. The
pressure of system seems to be unreasonable large, and during the whole
process, the box keeps increasing.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> Here is how I set up the system,<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> 1. I solvate the proteini use spc216.gro,
the log file shows: <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>
Output configuration contains 40990 atoms in 12386 residues<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>
Volume: 412.593 (nm ^3)<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>
Density: 1015.79 g/L<br clear=all>
Number of SOL
molecules: 13410<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal> 2. Then I start to do MD with constrains
(40 ps), then MD without constrains.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>
The md.log shows pressure keeps decrease, start from 5.79 e+02
until at last to about 3.14e+00, so you can see how large the box size is
enlarged.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> However in my setup, what
I use for P-coupling is the same:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>
Pcoupl = Berendsen<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>
Pcoupltype = isotropic<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> tau_p
= 0.5<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>
compressibility = 4.5e-5<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> ref_p
= 1.0<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal> my integral step size
is 1fs, so the tau_p = 0.5 ps should be enough. Also I checked the temperature,
it is constant during the MD process. (303K)<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> So from these setup
process, I think: the density is correct for solvent water and system; the
compressibility is chosen as for standard water, the ref_p is chosen as 1.0.
Why the pressure is so large?<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'> Thank
you in advance!<br>
-- <br>
Sincerely<br>
=================================<br>
Pan Wu<br>
Graduate Student in Department of Chemistry<br>
Duke University<br>
124 Science Drive<br>
5301 French Family Science Center<br>
Durham, NC 27708<br>
Phone: (919) 660-1583<br>
=================================<o:p></o:p></p>
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