AMBER Archive (2009)

Subject: RE: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB.

From: Niel Henriksen (niel.henriksen_at_utah.edu)
Date: Tue Jan 20 2009 - 14:49:38 CST

Hey Marek,
In regards to the NAB problems . . .

> // conjugate gradient minimization
> conjgrad(x, 3*m.natoms, fret, mme, 0.1, 0.001, 2 );
>
> // Newton-Raphson minimization\fP
> mm_options( "ntpr=1" );
> newton( x, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 2 );
>
> // get the normal modes:
> nmode( x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0);

The max iterations on your conjgrad command is 2. You probably need to make your rms gradient value smaller (maybe 0.0001) and increase the maxiter number (this depends, i've used 20000). You may also need to increase the maxiter for newton (I use 6) in order to achieve the target rms.

If there are still allocation errors . . . then hmmm . . .

- niel



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