[gmx-users] Problem with radius of gyration calculation
Ali Alizadeh
ali.alizadehmojarad at gmail.com
Thu Feb 6 13:32:11 CET 2014
Dear Jernej,
Why don't try using VMD for calculating RG?
--------------------
Jernej wrote:
Subject: [gmx-users] Problem with radius of gyration calculation
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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
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