[gmx-users] converting .xpm to .eps

[bipin singh]

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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>
> --
> 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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> posting!
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-- 



*--------------------Thanks and Regards,Bipin Singh*