[gmx-users] Problem with radius of gyration calculation

[Ali Alizadeh]

Dear Jernej,

Why don't try using VMD for calculating RG?

--------------------
Jernej wrote:
Subject: [gmx-users] Problem with radius of gyration calculation
Message-ID:
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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