Re: [AMBER] troubles in understanding, amber minimization input

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 24 Jan 2016 21:19:06 -0500

On Sun, Jan 24, 2016 at 2:04 PM, Saman Yousuf ali <
saman.yousufali64.yahoo.com> wrote:

> Dear Jason M. Swails,
>
> Thank you for your response. I knew that the restraint is not changed as
> the minimization progresses and to do this I must run all the minimization
> steps separately by gradually relaxing restraints on both protein and
> counter ions (25,20,15,10,5) and then unrestrained the whole system. I have
> performed total 6 minimization steps first 25 K Cal restrain with maxcycy
> 1000 then with 20 with maxcyc 1000 and so on. As you said that if I run 2
> minimizations, and both run for the full maxcyc, then I will get 2000 total
> minimization steps (assuming maxcyc=1000). So it means that I have
> performed total 6000 minimization step. Kindly correct me if I am wrong.
>

‚ÄčThat's what I would expect. Did you look at the output files? Each mdout
file should tell you how many steps the minimization completed.

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jan 24 2016 - 18:30:03 PST
Custom Search