[gmx-users] Re: Box-dimensions -g_energy_output
Kavyashree M
hmkvsri at gmail.com
Fri Jun 24 15:09:04 CEST 2011
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 have checked the entire file of the gmxdump output
of ener.edr firl for Box dimention as well as Temp.
Thanks
With Regards
M. Kavyashree
On Fri, Jun 24, 2011 at 6:32 PM, Justin A. Lemkul <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>> 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://vt.edu/Pages/Personal/justin>
>> >
>>
>> <http://www.bevanlab.biochem._**_
>> 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://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 | (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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