AMBER Archive (2009)

Subject: [AMBER] Regarding Minimization maxcyc

From: Ashish Runthala (ashish.runthala_at_gmail.com)
Date: Sun Aug 09 2009 - 09:09:58 CDT

Hello all,
Please answer me in detail.
How we set the upper limit of maxcyc during any minimization.
Generally which i have seen, the energies as a whole keeps changing
and there is not a constant energy minimization going altogether in
all the steps.
Thus it is possible, even after some maxcyc steps of our minimization
in any of steepest descent or conjugated gradient method, we may find
that some step number in between of the run is giving the minimum
energy.
So i was making a script to choose the minimum energy in the run out
of all displayed ntpr outputs in the output file to run the sander
again only till that step in the next iteration and finish the
minimization.

My query is . Is this correct way. As many a times, sander even though
being smart enough does not leap towards global minimum constantly
with decreasing energy in every single step.
I was having some ways to solve it in a better way.So first guide me,
in this first step so that i can implement the later steps too.
Correct me if i am wrong somewhere.

Regards
Ashish 

-- 
Ashish Runthala,
Faculty Division III,
Assistant Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA

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