AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Sep 25 2006 - 06:30:57 CDT

your energies are very high- something must be wrong with your
initial structure. we can't help with that since you didn't say how you
built it. it could also be that your refc isn't the same as your inpcrd.
we don't know since you didn't show the script.

Zhihong Yu 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
>
>
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