[gmx-users] Re: Box-dimensions -g_energy_output
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 24 15:02:17 CEST 2011
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 <hmkvsri at gmail.com
> <mailto:hmkvsri at gmail.com>> 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 <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> 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
> <hmkvsri at gmail.com <mailto:hmkvsri at gmail.com>
> <mailto:hmkvsri at gmail.com <mailto:hmkvsri at gmail.com>>
> <mailto:hmkvsri at gmail.com <mailto:hmkvsri at gmail.com>
> <mailto:hmkvsri at gmail.com <mailto:hmkvsri at gmail.com>>>> 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
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
> (540) 231-9080
>
>
> http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
> <http://vt.edu/Pages/Personal/justin>
>
> <http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
>
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> --
> ==============================__==========
>
> Justin A. Lemkul
> 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
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
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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