[gmx-users] Re: Box-dimensions -g_energy_output
Kavyashree M
hmkvsri at gmail.com
Fri Jun 24 15:03:19 CEST 2011
Sir,
Thats right. But what I felt was, all these
problems are connected. (I dont mean that
temperature is connected to box dimension)
Actually I was getting nan under RMSD for all
the energy terms.
I have checked the total energy graph also it
is stable.
even in case of box dimentions I checked the
box dimensions for the whole trajectory for eg.
Box-X most of the time has value around 9. very
few times it gets a value near 8.9..
Thank you
With Regards
M. Kavyashree
On Fri, Jun 24, 2011 at 6:18 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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://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>
>> >>
>>
>> ==============================**____==========
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>**>
>>
>>
>> http://lists.gromacs.org/____**mailman/listinfo/gmx-users<http://lists.gromacs.org/____mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>> >
>> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >>
>> Please search the archive at
>> http://www.gromacs.org/____**Support/Mailing_Lists/Search<http://www.gromacs.org/____Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>> >
>> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>>
>> before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >
>> <mailto:gmx-users-request at __gr**omacs.org <http://gromacs.org>
>> <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >>.
>>
>> Can't post? Read
>> http://www.gromacs.org/____**Support/Mailing_Lists<http://www.gromacs.org/____Support/Mailing_Lists>
>> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>> >
>> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>> >>
>>
>>
>>
>> -- ==============================**__==========
>>
>> 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>
>> >
>>
>> ==============================**__==========
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >
>> Please search the archive at
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>
>> before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >.
>> Can't post? Read http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>> >
>>
>>
>>
> --
> ==============================**==========
>
> 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>
>
> ==============================**==========
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110624/7047912d/attachment.html>
More information about the gromacs.org_gmx-users
mailing list