Thanks for your help. :)<br><br><div class="gmail_quote">On 23 March 2011 07:47, 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
Mark Abraham wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
On 23/03/2011 3:39 PM, Elisabeth wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks Mark for the hints. I am using a pre equilibrated box for both runs. Can you again explain how Can I interpret this from fluctuations from two runs? Below is the resutls from two versions: Thanks!<br>
</blockquote>
<br>
IIRC the contents of the .edr file didn't change across these versions, but the reporting of computed quantities did, so I'd make my life simpler and use only the 4.5.3 g_energy.<br>
<br>
</blockquote>
<br></div>
Actually, 4.5.3 may have the bug:<br>
<br>
<a href="http://redmine.gromacs.org/issues/696" target="_blank">http://redmine.gromacs.org/issues/696</a><br>
<br>
The quantities in the .edr file are correct, but the output from g_energy is nonsense. It was fixed for 4.5.4.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
Both simulations have a much higher value for the root-mean-squared deviation from the average (i.e. standard deviation) than for the average. So that means your data set looks something like "10000 20 6543 200 23444 23434 15 500 3444". Look at the .xvg file that is produced. You need a heck of a lot of such data to have confidence that your sample average reflects the true average. If you haven't got that pile of data, then you haven't observed the average with any confidence. This is normal for quantities computed from fluctuations in atomic positions. They're macroscopic quantities, and have to be observed over a lot of microscopic configurations.<br>
<br>
Be sure to check visually that your system is doing what you hope it is doing.<br>
<br>
Mark<br>
<br>
</div></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
<br>
4.0.7<br>
<br>
Statistics over 733801 steps [ 0.0000 thru 1467.6001 ps ], 1 data sets<br>
All averages are exact over 733801 steps<br>
<br>
Energy Average RMSD Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>
#Surf*SurfTen 203.778 3623.99 3623.98 -0.00203751 -2.99026<br>
<br>
<br>
Statistics over 483401 steps [ 500.0000 thru 1466.8000 ps ], 1 data sets<br>
All averages are exact over 483401 steps<br>
<br>
Energy Average RMSD Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>
#Surf*SurfTen 203.129 3612.58 3612.28 0.168686 163.086<br>
-----------------------------------------------------------------------------------------------------------------<br>
4.5.3<br>
<br>
<br>
<br>
Statistics over 732501 steps [ 1.0000 through 1466.0000 ps ], 1 data sets<br>
All statistics are over 73251 points<br>
<br>
Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
#Surf*SurfTen 2374.49 570 21081.3 -3251.38 (bar nm)<br>
<br>
Statistics over 384501 steps [ 1000.0000 through 1769.0000 ps ], 1 data sets<br>
All statistics are over 38451 points<br>
<br>
Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
#Surf*SurfTen 2610.25 1000 21109.9 4638.38 (bar nm)<br>
<br>
Statistics over 483001 steps [ 500.0000 through 1466.0000 ps ], 1 data sets<br>
All statistics are over 48301 points<br>
<br>
Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
#Surf*SurfTen 1645.07 390 20288.3 -174.289 (bar nm)<br>
<br>
<br>
<br>
<br>
<br></div></div><div class="im">
On 22 March 2011 23:56, 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>
<br>
<br>
On 23/03/11, *Elisabeth * <<a href="mailto:katesedate@gmail.com" target="_blank">katesedate@gmail.com</a><br></div><div class="im">
<mailto:<a href="mailto:katesedate@gmail.com" target="_blank">katesedate@gmail.com</a>>> wrote:<br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
<br>
On 22 March 2011 22:46, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div class="im">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Elisabeth wrote:<br>
<br>
<br>
<br>
On 22 March 2011 22:31, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><div><div></div><div class="h5"><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
Elisabeth wrote:<br>
<br>
Hello,<br>
I did two simulations on the same system using<br>
versions 4.0.7<br>
and 4.5.3. It seems like the unit of surface<br>
tension is not the<br>
same in these versions because I am getting ~250<br>
KJ/mol an in<br>
4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can<br>
be converted<br>
into bar nm? Can anyone help please.<br>
<br>
<br>
Is this from g_energy output? In past versions,<br>
everything was<br>
printed as "kJ/mol," even quantities that obviously<br>
weren't, like<br>
temperature, pressure, etc.<br>
<br>
<br>
Yes, so why are the results so different. I am using<br>
exactly the same mdp file.!<br>
<br>
<br>
Any pressure-related quantity is going to be subject to<br>
enormous fluctuations. This has been discussed within the<br>
last few days. Without seeing the .mdp file and a<br>
description of the system, it's hard for anyone to comment on<br>
what the results might mean.<br>
<br>
<br>
Thanks. I am working on a pure alkane system, in a box of 3X3X3<br>
which is extended in Z to create liq/air interface. That is 3X3X6<br>
. What could be reason for such a big difference in results from<br>
two version? Thanks alot! <br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
Look at the size of the fluctuations printed by g_energy. If<br>
they're comparable or larger than your differences, then you are<br>
not observing a statistically significant difference. Over just<br>
2ns of a small system, that's likely to be the case. Damping such<br>
fluctuations requires large simulations or long times or both.<br>
<br>
You are also generating velocities at the start of this run, so<br>
probably you are including spurious measurements on<br>
non-equilibrated configurations in your statistics. If you'd<br>
thought to tell us your command lines, I wouldn't be guessing :-)<br>
You can fix this with g_energy -b, but really you should separate<br>
your equilibration from your production run, even if you don't<br>
really need to, so that all your workflows have similar<br>
properties. Then when you come back to repeat some analysis in a<br>
month's time, you don't have to remember to ignore the first 1ns<br>
of this simulation...<br>
<br>
Mark<br>
<br>
<br>
</div></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
integrator = md dt = 0.002 nsteps = 1000000<br>
nstenergy = 100 nstxout = 100 nstlist = 10 ns_type = grid coulombtype = PME vdw-type = Shift rcoulomb-switch = 0 rvdw-switch = 0 rlist = 1.1 rcoulomb = 1.1 rvdw = 1.0 <br>
fourierspacing = 0.12 fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4 ewald_rtol = 1e-5<br>
;optimize_fft = yes<br>
Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 300 pbc = xyz gen_vel = yes gen_temp = 300.0 gen_seed = 173529 <br>
constraints = all-bonds constraint-algorithm = lincs<br>
<br>
<br>
-Justin<br>
<br>
<br>
<br>
-- ========================================<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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>
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<br>
-- <br>
========================================<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>
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