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

[Dr. Vitaly Chaban]

So there is a problem with your trajectory file. Try to understand what
kind of problem it is.

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.
>>>> >
>>>> --
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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
>