[gmx-users] converting .xpm to .eps

[Nidhi Jatana]

I tried increasing the grid spacing by setting -bin from default of 0.02 to
0.04 and decreased it as well to 0.01. Butives the same of no help. It
still gives the same error.


On Fri, Dec 20, 2013 at 4:19 PM, bipin singh <bipinelmat at gmail.com> wrote:

> You may try to produce the xpm matrix for small portion of your trajectory
> (using -b and -e option) and then try xpm2ps on it to check whether it
> works for small size xpm matrix or not.
>
>  OR you can increase the grid spacing with -bin option of g_densmap while
> generating the xpm matrix for the whole trajectory.
>
>
> On Fri, Dec 20, 2013 at 3:55 PM, Nidhi Jatana <nidhijatana at bic-svc.ac.in
> >wrote:
>
> > How do you fix the matrix size? Should I do it while generation of .xpm
> > file or while converting it to .eps and using which option?
> >
> > Regards
> > Nidhi
> >
> >
> > On Fri, Dec 20, 2013 at 3:35 PM, Carsten Kutzner <ckutzne at gwdg.de>
> wrote:
> >
> > > On 12/20/2013 10:09 AM, bipin singh wrote:
> > >
> > >> Not sure, might be something going wrong due to large dimension of
> your
> > >> matrix. Which Gromacs version you are using. Others may provide some
> > >> clues.
> > >>
> > > I just tried with a 483 x 486 matrix which went smoothly.
> > > You could try to narrow down the problem.
> > > See whether it works with other input data for example.
> > > Check whether it works on another machine.
> > >
> > > Carsten
> > >
> > >
> > >>
> > >> On Fri, Dec 20, 2013 at 10:04 AM, Nidhi Jatana <
> > nidhijatana at bic-svc.ac.in
> > >> >wrote:
> > >>
> > >>  Dear Sir/Madam
> > >>> Please find attached the file containing the error.
> > >>>
> > >>> Thanking you
> > >>>
> > >>> Regards
> > >>> --
> > >>> Nidhi Jatana
> > >>> Senior Research Fellow
> > >>> Bioinformatics Center
> > >>> Sri Venkateswara College
> > >>> (University of Delhi)
> > >>> Dhaula Kuan
> > >>> New Delhi-110021.
> > >>>
> > >>>
> > >>>
> > >>> On Thu, Dec 19, 2013 at 7:44 PM, Carsten Kutzner <ckutzne at gwdg.de>
> > >>> wrote:
> > >>>
> > >>>  On 12/19/2013 12:53 PM, Nidhi Jatana wrote:
> > >>>>
> > >>>>  Dear Sir/Madam
> > >>>>> I generated the atomic density plot using g_densmap by giving the
> > >>>>> following
> > >>>>> command:
> > >>>>> g_densmap -f *.xtc -s *.pdb -n *.ndx -o *.xpm
> > >>>>>
> > >>>>> The calculation completed successfully but when I am trying to
> > convert
> > >>>>> .xpm
> > >>>>> file to .eps file using xpm2ps command, its giving error and
> aborts.
> > >>>>>
> > >>>>>  What is the error message?
> > >>>>
> > >>>> If I use your set of commands with Gromacs 4.6.4, I can successfully
> > >>>>
> > >>> create
> > >>>
> > >>>> an EPS file.
> > >>>>
> > >>>> Carsten
> > >>>>
> > >>>>
> > >>>>  xpm2ps -f *.xpm -o *.eps -rainbow red -xpm *.xpm
> > >>>>>
> > >>>>> I have tried many options with setting -bx and -by but of no help.
> I
> > >>>>>
> > >>>> also
> > >>>
> > >>>> tried taking the .m2p file but the problem persist. Please find
> > attached
> > >>>>> the .m2p file for reference. Please help me with this.
> > >>>>>
> > >>>>> Thanking you
> > >>>>>
> > >>>>> Regards
> > >>>>>    --
> > >>>>> Nidhi Jatana
> > >>>>> Senior Research Fellow
> > >>>>> Bioinformatics Center
> > >>>>> Sri Venkateswara College
> > >>>>> (University of Delhi)
> > >>>>> Dhaula Kuan
> > >>>>> New Delhi-110021.
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>>  --
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> > >>>>
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> >
> > --
> > Nidhi Jatana
> > Senior Research Fellow
> > Bioinformatics Center
> > Sri Venkateswara College
> > (University of Delhi)
> > Dhaula Kuan
> > New Delhi-110021.
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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>
>
> --
>
>
>
> *--------------------Thanks and Regards,Bipin Singh*
> --
> Gromacs Users mailing list
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-- 
Nidhi Jatana
Senior Research Fellow
Bioinformatics Center
Sri Venkateswara College
(University of Delhi)
Dhaula Kuan
New Delhi-110021.