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

From: kenfack cyril <>
Date: Mon, 25 Jan 2016 08:00:27 +0000 (UTC)

Dear Amber users,I perform an MD simulation on a 15mers DNA duplex labeled in its central part with fluorescent probe, in a TIP3 water the probe can form H-bond with water molecules , i would like to know how to visualize my system  with all water molecules in h-bonding  interaction with the probe  along  the MD trajectory.thankBest regardCyril Kenfack Dr. KENFACK ASSONGO Cyril Centre for Atomic Molecular Physics and Quantum Optics (CEPAMOQ) Faculty of Science - University of Douala P.O. Box 8580 Douala - CAMEROON Tel. actuel : 0023796031051 Fax: 237) 3343 46 08 Email:

    On Monday, January 25, 2016 3:19 AM, Jason Swails <> wrote:

 On Sun, Jan 24, 2016 at 2:04 PM, Saman Yousuf ali <> 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.

​That'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
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 25 2016 - 00:30:04 PST
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