AMBER Archive (2009)

Subject: [AMBER] Discrepancy between AMBER and VMD calculation

From: Sunita Patel (sunita_iitb_at_yahoo.com)
Date: Thu Sep 17 2009 - 14:11:07 CDT

Dear amber-users,

I have performed REMD simulation on my system with implicit solvent simulation means there is no periodic boundary. I calculated radius of gyration of the molecule at a given temperature using both PTRAJ and VMD. I surprised seeing the different results of the same trajectory.
Why there is discrepancy in radius of gyration calculation using PTRAJ and VMD? Which one to rely?

Excerpt of the results
--------------------
PTRAJ (Rg)
#time RadGyr MaxRad
      0.00 11.562489 21.094724
      1.00 12.131283 21.432104
      2.00 11.767913 21.466811
      3.00 11.758013 21.665339
      4.00 15.281582 27.410967
      5.00 15.197682 28.285966
      6.00 11.558339 20.320215
      7.00 11.626524 19.649910
VMD (Rg)
0 17.736656189
1 21.5812740326
2 19.3697605133
3 17.5074920654
4 20.5340366364
5 20.5092773438
6 17.1818351746
7 17.4390163422

Regards,
Sunita

      
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