[gmx-users] Problems plotting gyrate.xvg

[Mark Abraham]

http://www.gromacs.org/Documentation/How-tos/Graphing_Data

On Tue, Aug 18, 2015 at 4:51 PM Daniela Rivas <dani.rivas.r at gmail.com>
wrote:

> 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.
> > >>> --
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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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