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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">My suggestion was to actually physically look at the data you are using to calculate the average. Make a graph of pressure versus time. Something as simple
as actually looking at the data can tell you a lot, rather than just pulling the average from somewhere.<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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";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;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>Sikandar Mashayak<br>
<b>Sent:</b> Wednesday, 28 September 2011 1:05 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] Pressure estimation from NVT<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hi<br>
<br>
@ Dallas and Justin <br>
<br>
Do you mean that for gromacs version 4.5.3 averages computed using g_energy may be flawed? And are you suggesting to compute average pressure explicitly from instantaneous P values in trajectory?
<br>
<br>
@ Mark<br>
<br>
Thanks for suggestion. I am doing 500 ps of equilibration and 10 ns of production runs with 2141 molecules.<br>
<br>
So the important point that I want to understand is that if I use the right averaging or newer gromacs version, and do large system with longer production runs, how accurate is the estimate of pressure values from bulk water NVT simulations?
<br>
<br>
thanks<br>
sikandar<o:p></o:p></p>
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<p class="MsoNormal">On Mon, Sep 26, 2011 at 8:51 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">On 27/09/2011 3:48 AM, Sikandar Mashayak wrote:<o:p></o:p></p>
<p class="MsoNormal">Hi<br>
<br>
I am trying to determine pressure of water at given density and temperature using SPC/E water model. To achieve this, I am doing NVT bulk simulations and then using g_energy I get average pressure values. The question I have is how accurate these average pressure
predictions are?<br>
<br>
e.g. I get average pressure of 185 bar for 300 K and 1 g/cm^3 water density, but theoretical value for it is around 1 bar. What are the possible reasons for this much deviation from theoretical value? Is there anything wrong with my set up? I am using 2141
water molecules in 4*4*4 periodic box, Nose-Hoover thermostat with 0.2ps time constant , MD algorithm with 1fs time-step, LJ with 1.5 nm cut off and PME for electrostatics.<o:p></o:p></p>
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<p class="MsoNormal">The length of your simulation, and the absence of the equilibration period from your data collection are also critical factors in obtaining accurate converged averages, but usually neglected when people report what might be anomalies...
please see <a href="http://www.gromacs.org/Documentation/Terminology/Pressure" target="_blank">
http://www.gromacs.org/Documentation/Terminology/Pressure</a><br>
<span style="color:#888888"><br>
Mark</span><o:p></o:p></p>
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