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.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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Received on Wed Sep 27 2006 - 06:07:15 PDT
