[gmx-users] Problems plotting gyrate.xvg

[Justin Lemkul]

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

==================================================