This is an update with the "image frequency" issue I posted a long time
ago. When the 'ntrun' parameter in nmode() was set to 1 (using dsyevd
routine to diagonalize the Hessian), all my 8 proteins had image
frequencies. However, in recent when I set 'ntrun' to 0, which uses the
dsyev routine to diagonalize the Hessian, all those image frequencies
disappeared.
Best
Junmei
On Wed, Oct 14, 2009 at 10:05 AM, Junmei Wang <junmwang.gmail.com> wrote:
> Hi, Everyone,
> When I ran normal mode analysis using nab for a set of ~100 residues
> protein structures, I found many of them have imaginary frequencies. Here is
> my calculation protocol:
>
> (1) remove waters, ions, and generate topologies
> (2) position-restrained GB minimization with a set of force constants: 20,
> 10, 5, 2, 0.0 (no restraint)
> (3) two-steps nab minimization using GB to reduce the RMS-gradient to
> ~1.0e-13
> (4) nma analysis
>
> To solve this problem, I added one more step to do some position-restrained
> GBMD (force constants are 20 and 10). But no help at all.
>
> Any suggestion how to solve the problem?
>
> Junmei
>
>
>
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Received on Wed Dec 09 2009 - 16:00:02 PST
