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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Received on Thu Sep 17 2009 - 12:30:02 PDT
