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

[Venkat Reddy]

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