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On 21/01/2011 10:12 AM, Denny Frost wrote:
<blockquote
cite="mid:AANLkTinhinDgU14Us9ymCvubXs4Cb8WuW+2-_jrP0jxf@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
In addition to all the points Justin mentioned, I'd observe that
you're generating velocities at the start of the run, so the system
will not be equilibrated for some time after that. See the advice
here
<a class="moz-txt-link-abbreviated" href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation">www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a>.
Anyway, you don't want to collect data for averages until after
equilibration.<br>
<br>
Secondly, tau-t of 0.1 is useful for equilibration, but a bit too
stringent for actual simulations. Using v-rescale T-coupling is
probably a good idea too.<br>
<br>
Until you address all these issues about the numerical quality of
your model of reality, hoping for observables to correlate with
reality is not justified.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTinhinDgU14Us9ymCvubXs4Cb8WuW+2-_jrP0jxf@mail.gmail.com"
type="cite">
<br>
<div class="gmail_quote">On Thu, Jan 20, 2011 at 3:51 PM, Dallas
Warren <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color:
rgb(31, 73, 125);">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: 11pt; color:
rgb(31, 73, 125);"><br>
Which one is it?</span></p>
<div class="im">
<p class="MsoNormal"><span style="font-size: 11pt;
color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
color: rgb(31, 73, 125);">Catch ya,<br>
<br>
Dr. Dallas Warren</span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
color: rgb(31, 73, 125);">Medicinal Chemistry and
Drug Action</span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
color: rgb(31, 73, 125);">Monash Institute of
Pharmaceutical Sciences</span><span
style="font-size: 10pt; color: rgb(31, 73, 125);">,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a moz-do-not-send="true"
href="mailto:dallas.warren@monash.edu"
target="_blank">dallas.warren@monash.edu</a></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
color: rgb(31, 73, 125);">+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: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt;
color: rgb(31, 73, 125);"> </span></p>
</div>
<div style="border-width: medium medium medium 1.5pt;
border-style: none none none solid; border-color:
-moz-use-text-color -moz-use-text-color
-moz-use-text-color blue; padding: 0cm 0cm 0cm 4pt;">
<div>
<div style="border-right: medium none; border-width:
1pt medium medium; border-style: solid none none;
border-color: rgb(181, 196, 223) -moz-use-text-color
-moz-use-text-color; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span style="font-size:
10pt;">From:</span></b><span style="font-size:
10pt;"> <a moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a>
[mailto:<a moz-do-not-send="true"
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: 12pt;">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 moz-do-not-send="true"
href="mailto:Dallas.Warren@monash.edu"
target="_blank">Dallas.Warren@monash.edu</a>>
wrote:</p>
</div>
<div>
<div class="h5">
<div>
<div>
<p class="MsoNormal"><span style="font-size:
11pt; color: rgb(31, 73, 125);">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:
11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size:
11pt; color: rgb(31, 73, 125);">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:
11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size:
11pt; color: rgb(31, 73, 125);">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:
11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size:
10pt; color: rgb(31, 73, 125);">Catch ya,<br>
<br>
Dr. Dallas Warren</span></p>
<p class="MsoNormal"><span style="font-size:
10pt; color: rgb(31, 73, 125);">Medicinal
Chemistry and Drug Action</span></p>
<p class="MsoNormal"><span style="font-size:
10pt; color: rgb(31, 73, 125);">Monash
Institute of Pharmaceutical Sciences,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a moz-do-not-send="true"
href="mailto:dallas.warren@monash.edu"
target="_blank">dallas.warren@monash.edu</a></span></p>
<p class="MsoNormal"><span style="font-size:
10pt; color: rgb(31, 73, 125);">+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: 11pt; color: rgb(31, 73,
125);"> </span></p>
<p class="MsoNormal"><span style="font-size:
11pt; color: rgb(31, 73, 125);"> </span></p>
<div style="border-width: medium medium medium
1.5pt; border-style: none none none solid;
border-color: -moz-use-text-color
-moz-use-text-color -moz-use-text-color
blue; padding: 0cm 0cm 0cm 4pt;">
<div>
<div style="border-right: medium none;
border-width: 1pt medium medium;
border-style: solid none none;
border-color: rgb(181, 196, 223)
-moz-use-text-color -moz-use-text-color;
padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt;">From:</span></b><span
style="font-size: 10pt;"> <a
moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a>
[mailto:<a moz-do-not-send="true"
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
moz-do-not-send="true"
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>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><br>
--</p>
<div class="im"><br>
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target="_blank">gmx-users@gromacs.org</a><br>
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<p class="MsoNormal"> </p>
</div>
</div>
</div>
<br>
--<br>
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</blockquote>
</div>
<br>
</blockquote>
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