AMBER Archive (2006)

Subject: Re: AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1?

From: David A. Case (case_at_scripps.edu)
Date: Thu May 11 2006 - 09:43:28 CDT

On Thu, May 11, 2006, Pan, Yongmei wrote:
>
> Here is one question on the structure minimization for nmode use. the drms
> from sander minimization with igb=1/2(GB) is about 1.0E-005, but it becomes
> 5 from nmode ntrun=1,

nmode doesn't know about generalized Born theory, so you hare using a
different force field in the two programs. You should not expect the
gradients or minima to be the same.

You could minimize in sander using an epsilon=4r model, then transfer things
to nmode. Or you could use NAB (http://www.scripps.edu/case) to get second
derivatives with a GB force field (at the expense of having to install and
learn a new program....)

...good luck....dac

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