[gmx-users] Re: Box-dimensions -g_energy_output
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 24 15:14:37 CEST 2011
Kavyashree M wrote:
> Sir.
>
> I am sorry for changing the topic. It was not intentional
> It just came as I wanted to mention the other part of the
> problem that data had.
I'm trying to focus the discussion because you've presented three separate
(maybe related) issues:
1. Wrong number of frames read
2. Wrong averages (in the case of box vectors)
3. Nonsensical standard deviations (in the case of temperature)
> I have checked the entire file of the gmxdump output
> of ener.edr firl for Box dimention as well as Temp.
>
If there's nothing suspicious, then try processing the file with g_energy from
4.5.4; if that gives the same problem then we can rule out g_energy being at
fault and the problem lies with the .edr file. But if you're saying that
everything is fine, then there's no clear solution. If I recall, you've said
other simulations you've done have given normal results. In that case, re-run
the simulation that's causing problems (or at least a short part of it, to test)
and see if you get usable output.
-Justin
> Thanks
> With Regards
> M. Kavyashree
>
>
> On Fri, Jun 24, 2011 at 6:32 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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> <mailto: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>
> <mailto: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>>
> <mailto: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>>>
> <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 <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>
> <http://vt.edu> |
>
> (540) 231-9080
>
>
> http://www.bevanlab.biochem.______vt.edu/Pages/Personal/justin
> <http://vt.edu/Pages/Personal/justin>
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> <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> <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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