[gmx-users] Problems plotting gyrate.xvg

Justin Lemkul jalemkul at vt.edu
Tue Aug 18 16:41:04 CEST 2015



On 8/18/15 10:39 AM, Daniela Rivas wrote:
> 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
>

By default, GROMACS produces XmGrace-formatted files.  It may not open in 
Gnuplot without some modification.

-Justin

>
> 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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>> 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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