[gmx-users] Problems plotting gyrate.xvg

[Smith, Micholas D.]

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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