Re: [AMBER] help in minimization

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 27 Jan 2015 11:17:30 -0500

On Tue, Jan 27, 2015 at 10:29 AM, Robin Jain <robinjain.chem.gmail.com>
wrote:

> dear all,
> I am simulating a system having a organic molecule in water. I want help in
> energy minimization step. I want to know that what must be the value of
> MAXCYC and NCYC. I used MAXCYC 200000 and NCYC 150000 so that the rms value
> be smaller than drms default value (1.0E-4). Am i right or wrong, please
> suggest .
>

‚ÄčThis depends on what you want to use the structure for. NCYC of 150K
seems wasteful to me, since steepest descent minimization is woefully
inefficient with regard to finding a local minimum. That said, 200K total
steps is (massive) overkill in my opinion if all you want to do is relax
bad contacts to start MD. But you can figure out how much minimization is
doing by looking at how the maximum gradient (which is the negative of the
largest force) changes and how the energy decays -- i.e., the standard
measures for the minimization of any target function.

You should also look through some available literature to see what other
people have done in similar studies as well as some standard texts in
computational chemistry, and experiment with different options
(particularly while working through the available tutorials). This mailing
list is not a replacement for a basic course in computational chemistry or
reviewing select literature -- after all, what we say is not peer-reviewed
(much), nor have we put as much time or effort into our response as
compared with professionally published work.

Good luck,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 27 2015 - 08:30:02 PST
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