From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Apr 01 2015 - 01:20:37 CDT
I am currently doing minimisation for a protein in water simply in a stepwise manner. For the first minimisation in which I fixed the protein and only water and ion could move, it worked fine. However for the second one in which I fixed water and backbone of the protein instead and let the side chains to relax, when I look at the energies using NamdPlot (https://www.dropbox.com/s/3kq9ql1z1l7wd9y/mini-2.png?dl=0 <https://www.dropbox.com/s/3kq9ql1z1l7wd9y/mini-2.png?dl=0>), it converges to two distinct energy values and jumps between them every few steps.
I have tried adjusting parameters like minBabyStep or minLineGoal. It does not alter the fact of bouncing energy values but changes the higher energy value, i.e. it now bounces from -1.0087e6 to -1.00865e6 instead of -1.0084e6.
I am wondering whether I am having problem with the protein structure or minimisation parameters.
Thanks in advance,
Department of Physics and Material Science
City University of Hong Kong
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