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

[Mark Abraham]

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
>>>>> 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
>>
> --
> 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