TMD on tRNA does not converge

From: Segun Jung (dauss75_at_gmail.com)
Date: Wed Mar 25 2009 - 11:13:21 CDT

Dear all,

 I have prepared the initial and native structure in explicit solvent
coupled with minimization and short dynamics. And now I am trying to do TMD
simulation, but the initial state does not converge to the native state.
Interestingly, the energy does not decrease significantly. Here are some of
the outputs followed by the NAMD script.

 TMD 1 40.1809 40.1822

ENERGY: 1 9327.7968 7564.7959 2571.4102 35.6150 -249623.6934 24037.9202
0.0000 0.0000 0.0000 -206086.1552 0.0000 -206086.1552 -206086.1552 0.0000
-8969.9874 -2796.3349 562430.4193 -8969.9874 -2796.3349

 .

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