[gmx-users] Re: RDF output has no data
Venkat Reddy
venkat4bt at gmail.com
Thu Apr 11 07:57:11 CEST 2013
Thank you sir for the valuable input. I will look into the matter and get
to you.
On Thu, Apr 11, 2013 at 2:40 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
> 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!
>>> > * 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
>>>
>>
>>
>>
>> --
>> 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
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