Re: TMD on tRNA does not converge

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Mar 25 2009 - 11:16:51 CDT

A major issue with parallel TMD runs is fixed in 2.7b1. Please test 2.7b1
and let us know if your issue is still present. Thanks.

-Jim

On Wed, 25 Mar 2009, Segun Jung wrote:

> 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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