AMBER Archive (2006)

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

From: Yongmei Pan (ypan2_at_uky.edu)
Date: Fri Jun 09 2006 - 22:03:26 CDT

Hi, guys

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!

Yongmei Pan
Pharmaceutical Sciences, University of Kentucky

Yongmei pan
College of pharmacy, University of Kentucky

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