Sir, <br><br>Thats right. But what I felt was, all these<br>problems are connected. (I dont mean that <br>temperature is connected to box dimension) <br>Actually I was getting nan under RMSD for all<br>the energy terms. <br>
<br>I have checked the total energy graph also it <br>is stable. <br>even in case of box dimentions I checked the <br>box dimensions for the whole trajectory for eg.<br>Box-X most of the time has value around 9. very<br>few times it gets a value near 8.9..<br>
<br>Thank you<br>With Regards<br>M. Kavyashree<br><br><div class="gmail_quote">On Fri, Jun 24, 2011 at 6:18 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;"><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><div class="im">
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>
</div></blockquote>
<br>
Let's keep on topic and focus on the box vectors; changing the subject midway makes it harder to arrive at a solution. The only diagnostic I can suggest is gmxdump. It should be rather obvious what's going on - your reported averages are 0.04, but the actual values from the plot are clearly different.<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">
Thanks<br>
With regards<br>
M. Kavyashree<br>
<br>
<br>
<br></div><div><div></div><div class="h5">
On Fri, Jun 24, 2011 at 5:20 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>
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<br>
energy frame read 50000 time 100000.000 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>
<br>
I've said several times before that this energy file is probably<br>
junk, and again I'd suspect that. The only thing to check would be<br>
to run gmxdump on the .edr file (and redirect into some output file<br>
or pipe the output through "more" to actually see it) and see where<br>
the energy values go screwy. If you find a bunch of nonsensical<br>
information, then you have your answer.<br>
<br>
-Justin<br>
<br>
Thank you fro answering.<br>
<br>
With Regards<br>
M. Kavyashree<br>
<br>
<br>
On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul<br>
<<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>><br></div></div><div><div></div><div class="h5">
<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>>>> 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<br>
anyone<br>
to offer you any useful help (as Mark said yesterday). For<br>
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>
<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>>><br>
<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>><br>
<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<br>
dimensions<br>
using g_energy this output was obtained -<br>
Statistics over 50000001 steps [ 0.0000 through<br>
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<br>
point are<br>
considered.<br>
Kindly give some suggestions.<br>
<br>
Thank you<br>
with regards<br>
M.Kavyashree<br>
<br>
<br>
<br>
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Justin A. Lemkul<br>
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Virginia Tech<br>
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ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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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>
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