Sir, <br><br>I went through the whole .edr file for one<br>specific term in which I was getting nan. <br>Of the three columns (Energy; Av. Energy; Sum Energy)<br>order (power) for temperature did not change at all in the<br>
first column but in the second column there was a change of<br>power between +1 and +2 which was +2 in another .edr file from <br>other simulation.<br>ven though the second column value is arround 1--e+02 while <br>those with +1 power is around 9.--e+01 which is quite near to<br>
1.--e+02.<br><br>But I did not find any huge changes in the temperature.<br><br>Thank you<br>With Regards<br>M. Kavyashree <br><br><div class="gmail_quote">On Fri, Jun 24, 2011 at 5:53 PM, Kavyashree M <span dir="ltr"><<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Sir, <br><br>I tried it already but It was huge file. this kind of nan comes only<br>for RMSD not for any other term. I will try looking into that file again.<br>
<br>Thanks<br>With regards<br><font color="#888888">M. Kavyashree</font><div><div></div><div class="h5"><br><br><br><br><div class="gmail_quote">
On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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><br>
<br>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Sir,<br>
<br>
I am sorry I did not get any mail for that query since I posted it.<br>
So I had to ask once again..<br>
<br>
1. g_energy -f ener.edr -o box.xvg<br>
selecting 15 16 17 0<br>
<br>
2. gmxcheck -e ener.edr<br>
<br>
Opened ener.edr as single precision energy file<br>
frame: 0 (index 0), t: 0.000 Last energy frame read 50000 time 100000.000 <br>
Found 50001 frames with a timestep of 2 ps.<br>
<br>
3. Gromacs version 4.5.3<br>
<br>
This is the same data where I was mentioning that I<br>
was getting "not a number" (nan) error for all<br>
energy calculations under RMSD section.<br>
<br>
</blockquote>
<br></div>
I've said several times before that this energy file is probably junk, and again I'd suspect that. The only thing to check would be to run gmxdump on the .edr file (and redirect into some output file or pipe the output through "more" to actually see it) and see where the energy values go screwy. If you find a bunch of nonsensical information, then you have your answer.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
Thank you fro answering.<br>
<br>
With Regards<br>
M. Kavyashree<br>
<br>
<br></div><div>
On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul <<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>>> wrote:<br>
<br>
<br>
<br>
Kavyashree M wrote:<br>
<br>
Dear users,<br>
<br>
Any suggestions?<br>
<br>
<br>
You haven't provided nearly enough diagnostic information for anyone<br>
to offer you any useful help (as Mark said yesterday). For example,<br>
please provide:<br>
<br>
1. Your exact g_energy command line<br>
2. The output of gmxcheck for this .edr file<br>
3. Your Gromacs version<br>
<br>
-Justin<br>
<br>
Thank you<br>
M. Kavyashree<br>
<br>
<br>
On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M<br>
<<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a> <mailto:<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>><br></div><div><div></div><div>
<mailto:<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a> <mailto:<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>>>> wrote:<br>
<br>
Dear users,<br>
<br>
In one of the simulations while calculating box dimensions<br>
using g_energy this output was obtained -<br>
Statistics over 50000001 steps [ 0.0000 through 100000.0000<br>
ps ], 3<br>
data sets<br>
All statistics are over 1978700 points<br>
<br>
Energy Average Err.Est. RMSD<br>
Tot-Drift<br>
------------------------------<u></u>__----------------------------<u></u>--__-------------------<br>
Box-X 0.0453229 1.8 0.637535 -9.93022 (nm)<br>
Box-Y 0.0453229 1.8 0.637535 -9.93022 (nm)<br>
Box-Z 0.0320482 1.3 0.450805 -7.02173 (nm)<br>
<br>
but the dimensions of the box is different. plot attached.<br>
I am not able to figure out why only 1978700 data point are<br>
considered.<br>
Kindly give some suggestions.<br>
<br>
Thank you<br>
with regards<br>
M.Kavyashree<br>
<br>
<br>
<br>
-- ==============================<u></u>__==========<br>
<br>
Justin A. Lemkul<br>
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ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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==============================<u></u>==========<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>
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