Facing issues in radius of gyration

[Shriyansh Srivastava]

Dear members

I have performed classical MD for 1 microsecond using Desmond. I am facing a discrepancy with regards to calculations of radius of gyration. While other descriptors (RMSD, RMSF) are in line with the trajectory movie, gyration values vary between 17 to 30 ang. I suspect that it is not in line with the trajectory.

I could not find anything regarding this on internet and thus the request for discussion. 

Attachments: gyration plot

[suyash pant]

Hello Shriyansh,

Can you try running the same after you re-centre your trajectory.

Please use this script from command line.

$SCHRODINGER/run trj_align.py -h

Let me know if this works.

Please make sure you have setup the environment variable for Desmond on your machine

Regards,

Suyash

[Shriyansh Srivastava]

Hey Suyash
Thank you so much, it worked. 
Attaching the figure.

Best 

Shriyansh

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