<meta charset="utf-8"><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Here is the mdp file<div><br></div><div><div>title = HEX</div><div>cpp = /lib/cpp</div>
<div>constraints = hbonds</div><div>integrator = md</div><div>dt = 0.002 ; ps !</div><div>nsteps = 2500000 ; total 5ns.</div><div>nstcomm = 10</div><div class="im" style="color: rgb(80, 0, 80); ">
<div>nstxout = 50000</div><div>nstvout = 50000</div><div>nstfout = 0</div><div>nstlog = 5000</div><div>nstenergy = 5000</div><div>nstxtcout = 25000</div>
<div>nstlist = 10</div><div>ns_type = grid</div><div>pbc = xyz</div></div><div>coulombtype = Cut-off</div><div>vdwtype = Cut-off</div><div>rlist = 1.2</div>
<div>rcoulomb = 1.2</div><div>rvdw = 1.2</div><div>fourierspacing = 0.12</div><div class="im" style="color: rgb(80, 0, 80); "><div>pme_order = 4</div><div>ewald_rtol = 1e-5</div>
<div>; Berendsen temperature coupling is on in two groups</div></div><div>Tcoupl = v-rescale</div><div>tc_grps = HEX </div><div>tau_t = 0.1 </div><div>ref_t = 300 </div>
<div>nsttcouple = 1</div><div>; Energy monitoring</div><div>energygrps = HEX </div><div class="im" style="color: rgb(80, 0, 80); "><div>; Isotropic pressure coupling is now on</div><div>Pcoupl = berendsen</div>
<div>pcoupltype = isotropic</div><div>;pc-grps = BMI PFF</div></div><div class="im" style="color: rgb(80, 0, 80); "><div>tau_p = 1.0</div><div>ref_p = 1.0</div><div>
compressibility = 4.5e-5</div><div><br></div></div><div class="im" style="color: rgb(80, 0, 80); "><div>; Generate velocites is off at 300 K.</div><div>gen_vel = yes</div><div>gen_temp = 300.0</div>
<div>gen_seed = 100000</div><div><br></div></div><div>This is the 'averages' section</div><div><br></div><div><div>"<span style="white-space: pre-wrap; "> </span><="<span style="white-space: pre-wrap; "> </span>===== ########<span style="white-space: pre-wrap; "> </span>####### ==><span style="white-space: pre-wrap; "> </span></div>
<div>"<span style="white-space: pre-wrap; "> </span><="<span style="white-space: pre-wrap; "> </span>=== A V E R A<span style="white-space: pre-wrap; "> </span>G E S ====><span style="white-space: pre-wrap; "> </span></div>
<div>"<span style="white-space: pre-wrap; "> </span><="<span style="white-space: pre-wrap; "> </span>= ############<span style="white-space: pre-wrap; "> </span>### ======><span style="white-space: pre-wrap; "> </span></div>
<div><span style="white-space: pre-wrap; "> </span></div><div>"<span style="white-space: pre-wrap; "> </span>St"<span style="white-space: pre-wrap; "> </span>atistics over 1<span style="white-space: pre-wrap; "> </span>0000001 steps u<span style="white-space: pre-wrap; "> </span>sing 10000001 f<span style="white-space: pre-wrap; "> </span>rames<span style="white-space: pre-wrap; "> </span></div>
<div><span style="white-space: pre-wrap; "> </span></div><div><span style="white-space: pre-wrap; "> </span>Energies (kJ/mo<span style="white-space: pre-wrap; "> </span>l)<span style="white-space: pre-wrap; "> </span></div>
<div><span style="white-space: pre-wrap; "> </span>Bond<span style="white-space: pre-wrap; "> </span>Angle Ry<span style="white-space: pre-wrap; "> </span>ckaert-Bell.<span style="white-space: pre-wrap; "> </span>LJ (SR)<span style="white-space: pre-wrap; "> </span>Coulomb (SR)</div>
<div><span style="white-space: pre-wrap; "> </span>4.57E+03<span style="white-space: pre-wrap; "> </span>3.62E+03<span style="white-space: pre-wrap; "> </span>3.34E+03<span style="white-space: pre-wrap; "> </span>-2.08E+04<span style="white-space: pre-wrap; "> </span>0.00E+00</div>
<div><span style="white-space: pre-wrap; "> </span>Potential<span style="white-space: pre-wrap; "> </span>Kinetic En.<span style="white-space: pre-wrap; "> </span>Total Energy<span style="white-space: pre-wrap; "> </span>Temperature<span style="white-space: pre-wrap; "> </span>Pressure (bar)</div>
<div><span style="white-space: pre-wrap; "> </span>-9.28E+03<span style="white-space: pre-wrap; "> </span>1.63E+04<span style="white-space: pre-wrap; "> </span>7.05E+03<span style="white-space: pre-wrap; "> </span>3.00E+02<span style="white-space: pre-wrap; "> </span>9.96E+02</div>
<div><span style="white-space: pre-wrap; "> </span></div><div><span style="white-space: pre-wrap; "> </span>Box-X<span style="white-space: pre-wrap; "> </span>Box-Y<span style="white-space: pre-wrap; "> </span>Box-Z<span style="white-space: pre-wrap; "> </span></div>
<div><span style="white-space: pre-wrap; "> </span>5.47E+00<span style="white-space: pre-wrap; "> </span>5.47E+00<span style="white-space: pre-wrap; "> </span>5.47E+00<span style="white-space: pre-wrap; "> </span></div><div>
<span style="white-space: pre-wrap; "> </span></div><div><span style="white-space: pre-wrap; "> </span>Total Virial (k<span style="white-space: pre-wrap; "> </span>J/mol)<span style="white-space: pre-wrap; "> </span></div>
<div><span style="white-space: pre-wrap; "> </span>5.44E+02<span style="white-space: pre-wrap; "> </span>-1.30E-01<span style="white-space: pre-wrap; "> </span>8.27E-02<span style="white-space: pre-wrap; "> </span></div>
<div><span style="white-space: pre-wrap; "> </span>-1.30E-01<span style="white-space: pre-wrap; "> </span>5.44E+02<span style="white-space: pre-wrap; "> </span>3.46E-02<span style="white-space: pre-wrap; "> </span></div>
<div><span style="white-space: pre-wrap; "> </span>8.27E-02<span style="white-space: pre-wrap; "> </span>3.46E-02<span style="white-space: pre-wrap; "> </span>5.44E+02<span style="white-space: pre-wrap; "> </span></div><div>
<span style="white-space: pre-wrap; "> </span></div><div><span style="white-space: pre-wrap; "> </span>Pressure (bar)<span style="white-space: pre-wrap; "> </span></div><div><span style="white-space: pre-wrap; "> </span>9.96E+02<span style="white-space: pre-wrap; "> </span>2.34E-02<span style="white-space: pre-wrap; "> </span>-1.51E-02<span style="white-space: pre-wrap; "> </span></div>
<div><span style="white-space: pre-wrap; "> </span>2.34E-02<span style="white-space: pre-wrap; "> </span>9.96E+02<span style="white-space: pre-wrap; "> </span>-2.77E-02<span style="white-space: pre-wrap; "> </span></div>
<div><span style="white-space: pre-wrap; "> </span>-1.51E-02<span style="white-space: pre-wrap; "> </span>-2.77E-02<span style="white-space: pre-wrap; "> </span>9.96E+02<span style="white-space: pre-wrap; "> </span></div>
<div><span style="white-space: pre-wrap; "> </span></div><div><span style="white-space: pre-wrap; "> </span>Total Dipole (D<span style="white-space: pre-wrap; "> </span>)<span style="white-space: pre-wrap; "> </span></div>
<div><span style="white-space: pre-wrap; "> </span>0.00E+00<span style="white-space: pre-wrap; "> </span>0.00E+00<span style="white-space: pre-wrap; "> </span>0.00E+00<span style="white-space: pre-wrap; "> </span></div></div>
<div><span style="white-space: pre-wrap; "><br></span></div><div><span style="white-space: pre-wrap; ">I</span> don't have an RMS section on my log file.</div><div>The final xvg file that comes from g_energy is much too long to post here, but contains exactly what is in the log file. The interactive output from g_energy is, however, thus:</div>
</div><div><br></div><div>Pressure = 995.9 bar (error = 0.65 bar)</div></span><br><div class="gmail_quote">On Tue, Feb 1, 2011 at 1:49 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Denny Frost wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Sorry to revisit this subject, but this output does not make sense. In the log file from my NPT simulation, the pressure readings fluctuate between about 300 bar and -300 bar, which I gather is pretty normal. However, at the end of the log file, it reports the average pressure being almost 1000 bar. g_energy also reports this value. In my mdp file, nstenergy is equal to nstlog, so the frequency of data is the same in the .edr file. How is is possible that the final average would be greater than any value obtained during the simulation?<br>
<br>
</blockquote>
<br></div>
As I recall from the previous discussion, there were lots of things wrong with your .mdp file and many things to troubleshoot. Can you please post:<br>
<br>
1. The .mdp file you're using<br>
2. The contents of the "AVERAGES" and "RMS FLUCTUATIONS" sections of your .log file<br>
3. The g_energy output (not the header stuff, just the actual meaningful result)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Thu, Jan 20, 2011 at 4:33 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
On 21/01/2011 10:12 AM, Denny Frost wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Sorry, I'm referring to a lot of runs here - some fluctuate more<br>
than others and some have greater average values than others. The<br>
average value is never greater than the maximum fluctuation in<br>
each run, so that is not a problem. The average given by<br>
g_energy, however, is not close to 1.0 bar in any of my runs.<br>
Some runs give an average pressure of 10 bar, some give an<br>
average value of -1000 bar.<br>
</blockquote>
<br>
In addition to all the points Justin mentioned, I'd observe that<br>
you're generating velocities at the start of the run, so the system<br>
will not be equilibrated for some time after that. See the advice<br>
here<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation" target="_blank">www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a><br></div>
<<a href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation" target="_blank">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a>>.<div class="im"><br>
Anyway, you don't want to collect data for averages until after<br>
equilibration.<br>
<br>
Secondly, tau-t of 0.1 is useful for equilibration, but a bit too<br>
stringent for actual simulations. Using v-rescale T-coupling is<br>
probably a good idea too.<br>
<br>
Until you address all these issues about the numerical quality of<br>
your model of reality, hoping for observables to correlate with<br>
reality is not justified.<br>
<br>
Mark<br>
<br>
<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
On Thu, Jan 20, 2011 at 3:51 PM, Dallas Warren<br></div><div class="im">
<<a href="mailto:Dallas.Warren@monash.edu" target="_blank">Dallas.Warren@monash.edu</a> <mailto:<a href="mailto:Dallas.Warren@monash.edu" target="_blank">Dallas.Warren@monash.edu</a>>> wrote:<br>
<br>
Then something you have said isn’t right. In first email you<br>
said that the pressure varies between -400 and +400 bar. Now<br>
you say that the average can vary from -1000 to +1000 bar. If<br>
the instantaneous pressure is varying from -1000 to +1000 bar,<br>
then that is not a real issue. However, if the average can be<br>
from -1000 to +1000 bar, then that definitely is.<br>
<br>
<br>
Which one is it?<br>
<br>
<br>
Catch ya,<br>
<br>
Dr. Dallas Warren<br>
<br>
Medicinal Chemistry and Drug Action<br>
<br>
Monash Institute of Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br></div>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a> <mailto:<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a>><div class="im"><br>
<br>
+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins<br>
to resemble a nail.<br>
<br>
<br>
*From:* <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>><br>
[mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>>] *On Behalf Of *Denny Frost<br>
*Sent:* Friday, 21 January 2011 9:23 AM<br>
*To:* Discussion list for GROMACS users<br>
*Subject:* Re: [gmx-users] Inaccurate pressure readings<br>
<br>
<br>
The average I calculate is not within -10 to 10, it is on the<br>
order of -1000 to 1000<br>
<br>
On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren<br></div>
<<a href="mailto:Dallas.Warren@monash.edu" target="_blank">Dallas.Warren@monash.edu</a> <mailto:<a href="mailto:Dallas.Warren@monash.edu" target="_blank">Dallas.Warren@monash.edu</a>>><div class="im">
<br>
wrote:<br>
<br>
You have a variable that is fluctuating over a range of 800+<br>
units (three orders of magnitude) and want the average to be 1.0?<br>
<br>
<br>
It is not a problem as such. If you can get a large enough<br>
data set of pressure data, and it will have to be very large,<br>
then you might get it close to one.<br>
<br>
<br>
But as long the average you calculate is within may be an<br>
order of magnitude (-10 to 10) then there is nothing to get<br>
too worried about.<br>
<br>
<br>
Catch ya,<br>
<br>
Dr. Dallas Warren<br>
<br>
Medicinal Chemistry and Drug Action<br>
<br>
Monash Institute of Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br></div>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a> <mailto:<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a>><div class="im"><br>
<br>
+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins<br>
to resemble a nail.<br>
<br>
<br>
*From:* <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>><br>
[mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a><br></div><div class="im">
<mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>>] *On Behalf Of *Denny Frost<br>
*Sent:* Friday, 21 January 2011 9:07 AM<br></div>
*To:* <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
*Subject:* [gmx-users] Inaccurate pressure readings<br>
<br>
<br>
I am running a variety of NPT simulations with polar,<br>
non-polar, and ionic compounds. Although my results for<br>
density agree well with experimental values, the pressures I<br>
get from g_energy are off by 1 to 3 orders of magnitude. In<br>
the log file, the pressure fluctuates around a lot from -400<br>
to 400 bar, which seems to be normal according to other posts<br>
on this list, but the average (which is what g_energy gives<br>
me) is not 1.0 bar, as I specified. Does anyone know how to<br>
correct this problem?<br>
<br>
<br>
Pressure coupling parameters:<br>
<br>
Pcoupl = berendsen<br>
<br>
pcoupltype = isotropic<br>
<br>
tau_p = 1.0<br>
<br>
ref_p = 1.0<br>
<br>
compressibility = 4.5e-5<br>
<br>
<br>
--<br>
<br>
<br>
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<br>
-- <br><div class="im">
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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