AMBER Archive (2006)

Subject: Re: AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied?

From: David A. Case (case_at_scripps.edu)
Date: Sat Jun 10 2006 - 12:06:49 CDT

On Fri, Jun 09, 2006, Yongmei Pan wrote:

>
> I use sander epsilon=4r model to do minimization for nmode ntrun=1. When
> there is no restraint, it works well; But when the backbone is restrained
> (it???s also restrained in nmode), there is small difference between the
> energies from sander min and nmode, which leads to the different rms
> gradients. That is to say, even if the rmsg in sander reaches for example,
> 1E-4, the rmsg from nmode just 1E-2. And this is the case when nmode won???t
> continue because the rmsg is bigger than the required rmsd. So is there any
> way to fix the problem? Thanks!

This problem has been discussed before, and the fix is here:
 
    http://amber.ch.ic.ac.uk/archive/200603/0265.html

Somehow, it looks like this never got posted as a bugfix....I'll put one
up soon. (The amber9 code has the fix as well).

...thanks...dac

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