From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Apr 02 2015 - 06:52:36 CDT
Well, are you really interested in the (local) minimum-energy coordinates?
If it were me, I couldn't care less, especially around that flexible loop.
If you really want to minimize, you can try switching back to conjugate
gradients.
Jerome
On 2 April 2015 at 05:26, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk> wrote:
> Thanks Jerome,
>
> Problem was solved by running more steps of sd. I have also loaded the
> trajectory and it was flipping of a flexible loop.
>
> However in fact with sd minimisation, the energy keeps decreasing instead
> of converges. I understand sd is a relatively "slow" minimisation but how
> can I tell when to stop? Now I have run more than 100,000 steps and I
> choose to step as the decrease of energy between steps was <0.01 kcal/mol--089e0112d06afcb8cb0512bc7861--
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