AMBER Archive (2009)

Subject: [AMBER] Problem with particle-mesh Ewald method

From: Yunjie Zhao (yjzhao.wh_at_gmail.com)
Date: Fri Mar 06 2009 - 21:29:02 CST

Hi everyone,

    Using Amber 9, I am trying to do molecular simulations in TIP3P explicit
solvent models. A cutoff of 9 angstrom is used to distinguish short-range
and long-range interactions, and long-range electrostatics were treated with
the particle-mesh Ewald method. The RNA molecule has 12 nt, 11 Na+ were
randomly placed. But it did not run.

    Here is the input file:
QMMM MD Script for Sander 9
&cntrl
imin=0, nstlim=10000000,
dt=0.002,
ntt=1, tempi=0.1, temp0=300.0,
ntb=1,
ntf=2, ntc=2,
cut=9.0,
ifqnt=1
/
&qmmm
qmmask=’1-12’,
qmtheory=1,
qmcut=9.0
/

   Here is the out file:
--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:

 getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 26.359
| New format PARM file being parsed.
| Version = 1.000 Date = 03/03/09 Time = 03:02:09
 NATOM = 11377 NTYPES = 17 NBONH = 11110 MBONA = 286
 NTHETH = 301 MTHETA = 445 NPHIH = 674 MPHIA = 812
 NHPARM = 0 NPARM = 0 NNB = 16813 NRES = 3682
 NBONA = 286 NTHETA = 445 NPHIA = 812 NUMBND = 37
 NUMANG = 72 NPTRA = 40 NATYP = 27 NPHB = 1
 IFBOX = 1 NMXRS = 34 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 630477
| Hollerith 71946
| Integer 295861
| Max Pairs 5047595
| nblistReal 136524
| nblist Int 510502
| Total 29140 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
LOADING THE QUANTUM ATOMS AS GROUPS

  Can anyone tell me how this is calculated?

Thanks!

Yunjie Zhao
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