AMBER Archive (2004)

Subject: Re: AMBER: questions about NMODE

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 28 2004 - 14:06:01 CDT

On Wed, Apr 28, 2004, xhu1_at_memphis.edu wrote:
>
> step 2. Because NR is generally not for a large system(NR works up to
> 60 residues in my case; for 80 residues, the job was not finished even
> after running 3 days), carry out conjugate gradient minimization using
> SANDER:
> a. DRMS=1.0E-5
> b. CUT=9999.
> c. NSNB=9999999
> d. MAXCYC=40000, NCYC=500

This looks fine.

>
> step 3. To avoid RMSD values problem between Newton-Rhapson and normal
> mode calcs, according to the answer at AMBER FAQ, I should write out
> the nonbonded pairlist during minimization and reading it back in the
> beginning of normal mode calculation.

This is not necessary with an "infinite" cutoff, as you are using.

>
> A. CG minimization stopped at cycle 10693 as following:
>
> ***********************************************************************
> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 10680 -1.9944E+03 2.1050E-05 3.3197E-04 CD
> 1050
>
> BOND = 49.1119 ANGLE = 192.7673 DIHED =
> 719.7927
> VDWAALS = -539.9797 EEL = -6284.0420 HBOND =
> 0.0000
> 1-4 VDW = 245.6998 1-4 EEL = 3622.2692 RESTRAINT =
> 0.0000

The above looks fine...should be plenty ready for normal mode analysis.

>
> C. At the amber7 manual, about NMODE gereral description(section 12.2,
> Page 248), it is mentioned "Use the double precision version for best
> convergence" when using SANDER to do CG minimization. Is there another
> version for double precision or just change code in somewhere?

This comment is outdated....sander is always and only double precision now.

It looks like you are ready to do the normal mode calculation.

...good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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