[gmx-users] Problems plotting gyrate.xvg

[Daniela Rivas]

Yes, I'm using gnuplot. I'll give it a try and see if that works. Thanks!

2015-08-18 11:42 GMT-03:00 Smith, Micholas D. <smithmd at ornl.gov>:

> Oh...
>
>
> So you are using gnuplot? The gyrate.xvg file is xmgrace native, so if you
> want to plot it with the built-in labels and such use xmgrace -nxy
> gyrate.xvg; if you want to use gnuplot, then you need to have it filter out
> all of the lines that have either "&" "#" and "@" symbols at the begining
> (though with the & you should stop otherwise you will have your second plot
> taken into the first).
>
> -Micholas
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Daniela
> Rivas <dani.rivas.r at gmail.com>
> Sent: Tuesday, August 18, 2015 10:39 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problems plotting gyrate.xvg
>
> Since version 4.6 it is not necessary to do so, it detects it automatically
> and it did. I didn't have problems obtaining the radius of gyration, I
> actually have it. I just have problems getting the plot using the command:
>
>  plot "gyrate.xvg" using 1:2 with lines
>
>
> 2015-08-18 11:23 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 8/18/15 10:13 AM, Daniela Rivas wrote:
> >
> >> Micholas,
> >>
> >> My input file is a DCD trajectory obtained in NAMD and I have gromacs
> >> 4.6.5.
> >>
> >>
> > One needs to specifically link against VMD's libraries when installing
> > GROMACS for reading non-GROMACS formats if you want to read, e.g. DCD.
> >
> > -Justin
> >
> >
> > 2015-08-18 11:07 GMT-03:00 Smith, Micholas D. <smithmd at ornl.gov>:
> >>
> >> Daniela,
> >>>
> >>> What exact is your input? And what version of gromacs?
> >>>
> >>> ===================
> >>> Micholas Dean Smith, PhD.
> >>> Post-doctoral Research Associate
> >>> University of Tennessee/Oak Ridge National Laboratory
> >>> Center for Molecular Biophysics
> >>>
> >>> ________________________________________
> >>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> >>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> Daniela
> >>> Rivas <dani.rivas.r at gmail.com>
> >>> Sent: Tuesday, August 18, 2015 10:00 AM
> >>> To: gromacs.org_gmx-users at maillist.sys.kth.se
> >>> Subject: [gmx-users] Problems plotting gyrate.xvg
> >>>
> >>> Hi,
> >>>
> >>> I've been trying to plot the radius of gyration I got using gromacs,
> but
> >>> I
> >>> keep getting the segmentation fault. What does this mean? I have plenty
> >>> memory (32 TB), so it can't be a memory problem.
> >>>
> >>> My trajectory has 40000 frames (20 ns simulation) and I'm calculating
> the
> >>> radius of gyration of my protein (~7000 atoms).
> >>>
> >>> Thanks in advance.
> >>>
> >>> Daniela.
> >>> --
> >>> Gromacs Users mailing list
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> >>>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> >
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