Sorry, I'm referring to a lot of runs here - some fluctuate more than others and some have greater average values than others. The average value is never greater than the maximum fluctuation in each run, so that is not a problem. The average given by g_energy, however, is not close to 1.0 bar in any of my runs. Some runs give an average pressure of 10 bar, some give an average value of -1000 bar.<br>
<br><div class="gmail_quote">On Thu, Jan 20, 2011 at 3:51 PM, Dallas Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Then something you have said isn’t right. In first email you said that the pressure varies between -400 and +400 bar. Now you say that the average can vary from -1000 to +1000 bar. If the instantaneous pressure is varying from -1000 to +1000 bar, then that is not a real issue. However, if the average can be from -1000 to +1000 bar, then that definitely is.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><br>Which one is it?</span></p><div class="im"><p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p><p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Catch ya,<br>
<br>Dr. Dallas Warren</span></p><p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Medicinal Chemistry and Drug Action</span></p><p class="MsoNormal"><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><a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a></span></p><p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">+61 3 9903 9304<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;color:#1F497D"> </span></p><p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p>
</div><div style="border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt"><div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"><p class="MsoNormal"><b><span style="font-size:10.0pt">From:</span></b><span style="font-size:10.0pt"> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] <b>On Behalf Of </b>Denny Frost<br>
<b>Sent:</b> Friday, 21 January 2011 9:23 AM<br><b>To:</b> Discussion list for GROMACS users<br><b>Subject:</b> Re: [gmx-users] Inaccurate pressure readings</span></p></div></div><div class="im"><p class="MsoNormal"> </p>
<p class="MsoNormal" style="margin-bottom:12.0pt">The average I calculate is not within -10 to 10, it is on the order of -1000 to 1000</p></div><div><div class="im"><p class="MsoNormal">On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren <<a href="mailto:Dallas.Warren@monash.edu" target="_blank">Dallas.Warren@monash.edu</a>> wrote:</p>
</div><div><div></div><div class="h5"><div><div><p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">You have a variable that is fluctuating over a range of 800+ units (three orders of magnitude) and want the average to be 1.0?</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p><p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">It is not a problem as such. If you can get a large enough data set of pressure data, and it will have to be very large, then you might get it close to one.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p><p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">But as long the average you calculate is within may be an order of magnitude (-10 to 10) then there is nothing to get too worried about.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p><p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Catch ya,<br><br>Dr. Dallas Warren</span></p><p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Medicinal Chemistry and Drug Action</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Monash Institute of Pharmaceutical Sciences, Monash University<br>381 Royal Parade, Parkville VIC 3010<br><a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">+61 3 9903 9304<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;color:#1F497D"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p><div style="border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt"><div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-size:10.0pt">From:</span></b><span style="font-size:10.0pt"> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] <b>On Behalf Of </b>Denny Frost<br>
<b>Sent:</b> Friday, 21 January 2011 9:07 AM<br><b>To:</b> <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><b>Subject:</b> [gmx-users] Inaccurate pressure readings</span></p></div></div>
<div><p class="MsoNormal"> </p><p class="MsoNormal">I am running a variety of NPT simulations with polar, non-polar, and ionic compounds. Although my results for density agree well with experimental values, the pressures I get from g_energy are off by 1 to 3 orders of magnitude. In the log file, the pressure fluctuates around a lot from -400 to 400 bar, which seems to be normal according to other posts on this list, but the average (which is what g_energy gives me) is not 1.0 bar, as I specified. Does anyone know how to correct this problem?</p>
<div><p class="MsoNormal"> </p></div></div><div><p class="MsoNormal">Pressure coupling parameters:</p></div><div><div><div><p class="MsoNormal">Pcoupl = berendsen</p></div><div><p class="MsoNormal">pcoupltype = isotropic</p>
</div><div><p class="MsoNormal">tau_p = 1.0</p></div><div><p class="MsoNormal">ref_p = 1.0</p></div><div><p class="MsoNormal">compressibility = 4.5e-5</p></div></div></div></div>
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