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

[Dr. Vitaly Chaban]

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
>