[gmx-users] Re: Box-dimensions -g_energy_output
Kavyashree M
hmkvsri at gmail.com
Fri Jun 24 14:23:53 CEST 2011
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> 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>> 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>>> 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> | (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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