[gmx-users] Problem with radius of gyration calculation

[João Henriques]

First of all, Justin is right. Without commands and exact selections we
can't help much.

Second: "Why don't try using VMD for calculating RG?" - I ask the opposite,
ie. why use VMD when you got a native tools to do such? It's like using
genuine Nespresso capsules on a white-label machine when you have the real
one at an arm's length reach.

"Now, I'trying to compute the radius of gyration of one of these
molecules." + "I checked the index file and all the atoms are accounted for."
- My money goes on the index file and the input selection. g_gyrate should
work fine for one polymer given a proper index file and selection.

In sum, please provide further information.

Cheers,
João


On Thu, Feb 6, 2014 at 2:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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