[gmx-users] Problem with radius of gyration calculation

[Justin Lemkul]

On 2/6/14, 3:26 AM, Jernej Zidar wrote:
> 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.
>

Please supply the exact commands and the actual selections you are making rather 
than an interpretation of what's going on - you'll get a solution much faster!

Are you trying to analyze all of the polymers at once, or just one of the 
chains?  Is there solvent in the trajectory or has it been removed?

g_polystat is probably a better tool for polymer analysis.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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