Kavyashree M wrote:
Sir,
I went through the whole .edr file for one
specific term in which I was getting nan.
Of the three columns (Energy; Av. Energy; Sum Energy)
order (power) for temperature did not change at all in the
first column but in the second column there was a change of
power between +1 and +2 which was +2 in another .edr file from
other simulation.
ven though the second column value is arround 1--e+02 while
those with +1 power is around 9.--e+01 which is quite near to
1.--e+02.
But I did not find any huge changes in the temperature.
Per my previous message, please focus on the issue at hand. I do not recall the
specifics of the issue with temperature and I'm not going to go digging through
the archive for messages scattered over many days. You started this thread
regarding box vectors, for which we have the data below in the thread. Please
keep the discussion focused. If you jump around between ideas with somewhat
abstract descriptions, no one is going to be interested in troubleshooting. If
you want free help, make it easy to help you.
If you have something relevant to post regarding box vectors, please do so,
otherwise, if you want to investigate a different issue please give it proper
context (new thread or including information from the old thread).
Actual output would be useful, although I realize that may be too large of a
message to send across the list, so snippets that illustrate anything useful
would be appropriate.
-Justin
Thank you
With Regards
M. Kavyashree
On Fri, Jun 24, 2011 at 5:53 PM, Kavyashree M <[email protected]
<mailto:[email protected]>> wrote:
Sir,
I tried it already but It was huge file. this kind of nan comes only
for RMSD not for any other term. I will try looking into that file
again.
Thanks
With regards
M. Kavyashree
On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Kavyashree M wrote:
Sir,
I am sorry I did not get any mail for that query since I
posted it.
So I had to ask once again..
1. g_energy -f ener.edr -o box.xvg
selecting 15 16 17 0
2. gmxcheck -e ener.edr
Opened ener.edr as single precision energy file
frame: 0 (index 0), t: 0.000 Last
energy frame read 50000 time 100000.000
Found 50001 frames with a timestep of 2 ps.
3. Gromacs version 4.5.3
This is the same data where I was mentioning that I
was getting "not a number" (nan) error for all
energy calculations under RMSD section.
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.
-Justin
Thank you fro answering.
With Regards
M. Kavyashree
On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
Kavyashree M wrote:
Dear users,
Any suggestions?
You haven't provided nearly enough diagnostic information
for anyone
to offer you any useful help (as Mark said yesterday).
For example,
please provide:
1. Your exact g_energy command line
2. The output of gmxcheck for this .edr file
3. Your Gromacs version
-Justin
Thank you
M. Kavyashree
On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>> wrote:
Dear users,
In one of the simulations while calculating box
dimensions
using g_energy this output was obtained -
Statistics over 50000001 steps [ 0.0000 through
100000.0000
ps ], 3
data sets
All statistics are over 1978700 points
Energy Average Err.Est.
RMSD
Tot-Drift
------------------------------____----------------------------__--__-------------------
Box-X 0.0453229 1.8
0.637535 -9.93022 (nm)
Box-Y 0.0453229 1.8
0.637535 -9.93022 (nm)
Box-Z 0.0320482 1.3
0.450805 -7.02173 (nm)
but the dimensions of the box is different. plot
attached.
I am not able to figure out why only 1978700 data
point are
considered.
Kindly give some suggestions.
Thank you
with regards
M.Kavyashree
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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