[gmx-users] Problems plotting gyrate.xvg

Felipe Merino felipe.merino at mpi-dortmund.mpg.de
Tue Aug 18 16:42:11 CEST 2015


So unless the file is corrupted or empty, this is a gnuplot problem and 
not a gromacs one. Check inside your gyrate file with a text editor to 
see if it is correct.

On 18/08/15 16:39, 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
>
>
> 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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-- 
Felipe Merino
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2306



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