From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Apr 01 2015 - 02:14:12 CDT
Hi Kevin,
Two things you can try:
1) open that trajectory in VMD and see exactly what is oscillating, just in
case it indicates a deeper problem;
2) run a few steps of steepest descent.
Jerome
On 1 April 2015 at 08:20, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk> wrote:
> Dear Users,
>
> 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), 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,
>
>
>
> Kevin
> PhD Candidate
> Department of Physics and Material Science
> City University of Hong Kong
> ukevi_at_gmx.hk
>
>
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