AMBER Archive (2006)

Subject: Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Mon Sep 25 2006 - 14:28:55 CDT

Hi Zhihong,

Your force constant is also too small. If you used the same value for your
"stage 1" minimization, your solute probably had been destroyed. You can
try with a large force constant, say 500, for your constrained
minimization.

Regards!

Liu

On Sun, 24 Sep 2006 23:03:28 -0400, Zhihong Yu
<computation_at_mail.nankai.edu.cn> wrote:

> Dear All,
>
> As general MD procedures, I've finished the "Minimisation Stage 1 -
> Holding the solute fixed" and got a "relaxwater_min.rst" file, then I
> perform the "Minimisation Stage 2 - Minimising the entire system" based
> on this "relaxwater_min.rst", because I want to restrained all residues
> in 15~20 shell of an inhibitor.[the method is described in detail on the
> page 4575 in professor simmerling's paper(J. Med. Chem. 2006, 49,
> 4574-4580)] so I write mdin file as follow:
>
> Hold the 15-20 A shell and relax others
> &cntrl
> imin = 1, ncyc = 1000, maxcyc = 3000,
> ntb = 1, ntr = 1
> /
> Hold the 15~20A shell fixed part01
> 0.5
> RES 144 160
> END
> .....(other 31 restrained parts are omitted here)
> Hold the 15~20A shell fixed part33
> 0.5
> ERS 521 525
> END
> END
>
> my system include 27083 atoms, and I ran this minimisation by PMEMD
> version 9 on 8 nodes, after about 1 hours, the computation looks like to
> be choked, so I killed the job, checked the mdout file (attached as
> relaxsystem.out) and found out ".... RESTARTED DUE TO LINMIN FAILURE
> ...", I've searched this "LINMIN FAILURE" on this mail list and found
> that it's not a very serious problem. But after checking the mdout file,
> I found out another strange thing about the energy of "1-4 EEL" and
> "EAMBER", in many steps they were represented by "*************", I
> think it's just too big to display. Moreover, form the NSTEP of 150, the
> RMS increased to 5.2082E+10, it seems that these values were abnormal,
> whether it means our system have some serious problem? or my mdin file
> have some problem?
>
>
>
> Any advice will be greatly appreciated! Thanks in advance & Best
> regards!
>
> yours sincerely, Zhihong Yu 

-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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