[gmx-users] Re: RDF output has no data

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 10 23:10:38 CEST 2013 

You have a box with negligible dimensions, so as forecast above, your
conversion process from AMBER was not as effective as it might have been.
As you can see with g_rdf -h, it defaults to using periodic boundary
conditions. You need to do something different.

Mark


On Wed, Apr 10, 2013 at 2:38 PM, Venkat Reddy <venkat4bt at gmail.com> wrote:

> Sir
>
> I truncated my file so it has only 10 molecules of water and 5 frames.
> gmxcheck gives the following information
> Checking file test.trr
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time    0.000
> # Atoms  30
> Last frame          5 time    0.500
>
>
> Item        #frames Timestep (ps)
> Step             6    0.1
> Time             6    0.1
> Lambda           6    0.1
> Coords           6    0.1
> Velocities       0
> Forces           0
> Box              6    0.1
>
> And the output file for gmxdump is attached. They look fine in my limited
> knowledge of gromacs that I have gained in the past couple of days.
>
> Please advice
>
>
> On Tue, Apr 9, 2013 at 6:39 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban <vvchaban at gmail.com>
>> wrote:
>> > So there is a problem with your trajectory file. Try to understand what
>> > kind of problem it is.
>>
>> e.g. by using gmxcheck and/or gmxdump (on a small version of your
>> data!) to see what information is present.
>>
>> Mark
>>
>> >
>> > I can recollect that I experienced something like that why translating
>> CPMD
>> > trajectory to GROMACS. Maybe, it does not write time for each frame at
>> the
>> > right place -- just a guess.
>> >
>> > Dr. Vitaly Chaban
>> >
>> >
>> >
>> >
>> > On Tue, Apr 9, 2013 at 7:44 AM, Venkat Reddy <venkat4bt at gmail.com>
>> wrote:
>> >
>> >> Sir
>> >>
>> >> I tried g_msd, after asking for group selection the program appears
>> not to
>> >> read the frames as it remains stuck at reading frame 0, time 0.00.
>> >>
>> >> What to do?
>> >>
>> >> Thanks
>> >>
>> >>
>> >>
>> >>
>> >> On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban <vvchaban at gmail.com
>> >wrote:
>> >>
>> >>> Do you experience this problem with g_rdf only, or with all gromacs
>> >>> analysis utilities?
>> >>>
>> >>>
>> >>> On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy <venkat4bt at gmail.com>
>> wrote:
>> >>>
>> >>>> Sir
>> >>>>
>> >>>> I loaded the trajectory. There doesn't seem to be anything wrong with
>> >>>> it. Have no clue whats going wrong
>> >>>>
>> >>>> Thanks
>> >>>>
>> >>>>
>> >>>> On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban <
>> vvchaban at gmail.com>wrote:
>> >>>>
>> >>>>> I believe the problem is in the way which you used to convert AMBER
>> >>>>> trajectory to the GROMACS trajectory....
>> >>>>>
>> >>>>> I would suggest to try gmxdump and see what your trajectory looks
>> like.
>> >>>>> Oe
>> >>>>> maybe even better - try to visualize it in VMD to see if the format
>> is
>> >>>>> correct.
>> >>>>>
>> >>>>> Dr. Vitaly Chaban
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> Sir
>> >>>>> >
>> >>>>> > I was using an old version. Now I used 4.5.5, it still gives me
>> the
>> >>>>> same
>> >>>>> > blank output file.
>> >>>>> >
>> >>>>> > Kindly suggest how to go about solving this
>> >>>>> >
>> >>>>> > Thanks
>> >>>>> >
>> >>>>> >
>> >>>>> > On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham <
>> >>>>> mark.j.abraham at gmail.com
>> >>>>> > >wrote:
>> >>>>> >
>> >>>>> > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy <
>> venkat4bt at gmail.com>
>> >>>>> > wrote:
>> >>>>> > >
>> >>>>> > > > There was no fatal error preceding the output. After
>> selecting the
>> >>>>> > groups
>> >>>>> > > > following are the output on the screen
>> >>>>> > > > Reading frame       1 time    0.100
>> >>>>> > > > Warning: can not make broken molecules whole without a run
>> input
>> >>>>> file,
>> >>>>> > > >          don't worry, mdrun doesn't write broken molecules
>> >>>>> > > >
>> >>>>> > >
>> >>>>> > > This message is from a prehistoric version of g_rdf. Please get
>> a
>> >>>>> new
>> >>>>> > one.
>> >>>>> > >
>> >>>>> > > Mark
>> >>>>> > >
>> >>>>> > >
>> >>>>> > > >
>> >>>>> > > > Reading frame    2000 time  200.000
>> >>>>> > > >
>> >>>>> > > >
>> >>>>> > > > gcq#69: "The Wheels On the Bus Go Round and Round" (J.
>> Richman)
>> >>>>> > > >
>> >>>>> > > > And the rdf.xvg file looks like this
>> >>>>> > > >
>> >>>>> > > > #This file was created Sat Apr  6 10:54:13 2013
>> >>>>> > > > # by the following command:
>> >>>>> > > > # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg
>> >>>>> > > > #
>> >>>>> > > > # g_rdf is part of G R O M A C S:
>> >>>>> > > > #
>> >>>>> > > > # GROningen MAchine for Chemical Simulation
>> >>>>> > > > #
>> >>>>> > > > @    title "Radial Distribution"
>> >>>>> > > > @    xaxis  label "r"
>> >>>>> > > > @    yaxis  label ""
>> >>>>> > > > @TYPE xy
>> >>>>> > > > @ subtitle "O21-H2_&_CAT"
>> >>>>> > > >      0.001          1
>> >>>>> > > > ~
>> >>>>> > > >
>> >>>>> > > > Whats going wrong? Please help.
>> >>>>> >
>> >>>>> --
>> >>>>> gmx-users mailing list    gmx-users at gromacs.org
>> >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>>> * Please search the archive at
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>> >>>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> --
>> >>>> With Best Wishes
>> >>>> Venkat Reddy Chirasani
>> >>>> PhD student
>> >>>> Laboratory of Computational Biophysics
>> >>>> Department of Biotechnology
>> >>>> IIT Madras
>> >>>> Chennai
>> >>>> INDIA-600036
>> >>>>
>> >>>
>> >>>
>> >>
>> >>
>> >> --
>> >> With Best Wishes
>> >> Venkat Reddy Chirasani
>> >> PhD student
>> >> Laboratory of Computational Biophysics
>> >> Department of Biotechnology
>> >> IIT Madras
>> >> Chennai
>> >> INDIA-600036
>> >>
>> > --
>> > gmx-users mailing list    gmx-users at gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> > www interface or send it to gmx-users-request at gromacs.org.
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
>

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