[gmx-users] Problems plotting gyrate.xvg

[Smith, Micholas D.]

Daniela,

I believe your issue is the DCD file, as I look at the help for g_gyrate (from 4.6.5), I don't see a compatability with DCD. You could convert it to a pdb and then using g_gyrate and see if that fixes the issue.

-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 10:13 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Problems plotting gyrate.xvg

Micholas,

My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5.

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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