Kavyashree M 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.
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.
-Justin
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
-- ==============================____==========
Justin A. Lemkul
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Virginia Tech
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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