[gmx-users] Re: Box-dimensions -g_energy_output
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 24 14:48:52 CEST 2011
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 <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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