[gmx-users] Problem with radius of gyration calculation
Ali Alizadeh
ali.alizadehmojarad at gmail.com
Thu Feb 6 17:02:27 CET 2014
VMD is an alternative, it was my suggestion. I know my similar was similar
to ignoring the original questions.
Besides, he can calculate end to end distance if he wants. Anyway, you are
right:).
On Thu, Feb 6, 2014 at 4:32 AM, Ali Alizadeh
<ali.alizadehmojarad at gmail.com>wrote:
> Dear Jernej,
>
> Why don't try using VMD for calculating RG?
>
> --------------------
> Jernej wrote:
> Subject: [gmx-users] Problem with radius of gyration calculation
> Message-ID:
> <CAANrtrJLdyrA1adXN2_Jc8th=
> NpxRwME-pyABU9ue4W0eANMkg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> I have a polymer system composed of three molecules (I generated it
> by taking one molecule and 'copied' along the y axis). Now, I'trying
> to compute the radius of gyration of one of these molecules. When I do
> the analysis for the smallest system, composed of 483 atoms (i.e. 161
> atoms/molecule), I see the following messages appearing on the screen:
> Reading frame 0 time 0.000 There were 2 inconsistent
> shifts. Check your topology
> There were 2 inconsistent shifts. Check your topology
> Reading frame 1 time 20.000 There were 2 inconsistent
> shifts. Check your topology
> There were 2 inconsistent shifts. Check your topology
> Reading frame 2 time 40.000 There were 2 inconsistent
> shifts. Check your topology
> There were 2 inconsistent shifts. Check your topology
> Reading frame 3 time 60.000 There were 2 inconsistent
> shifts. Check your topology
> There were 2 inconsistent shifts. Check your topology
> Reading frame 7 time 140.000 There were 2 inconsistent
> shifts. Check your topology
> There were 2 inconsistent shifts. Check your topology
> Reading frame 8 time 160.000 There were 2 inconsistent
> shifts. Check your topology
> There were 2 inconsistent shifts. Check your topology
>
> What do these messages mean? To g_gyrate I supply the TPR file that
> was used for the production run, the compressed trajectory of this run
> and an index file containing the relevant inidices. I checked the
> index file and all the atoms are accounted for. Nothing suspicious is
> happening if I visualize the trajectory.
>
> Thanks in advance for any help!
>
> Jernej
> --
> Sincerely
>
> Ali Alizadeh
>
>
--
Sincerely
Ali Alizadeh
University of Tehran
College of engineering(Fanni)
Department of chemical engineering
IPE (Institute of Petroleum Engineering)
M.Sc Candidate, class of 2013
B.Sc Graduate 2011(University of Tehran,Fanni)
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