AMBER Archive (2009)

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

From: steinbrt_at_rci.rutgers.edu
Date: Fri Mar 06 2009 - 21:42:26 CST

Hi,

hard to tell whats going on from the information you present. Have you
tried running the system without QM potentials turned on? Can you run
smaller QM/MM systems? Can you run just a short minimization of your
system? Why do you think this is an Ewald problem? Do the QM/MM test cases
all run through?

Just one thing that might be it: Your QMMASK is specified as '1-12'. I
guess that should be '@1-12' to specify the first 12 atoms or ':1-12' for
the first 12 residues (which would be a pretty big QM system...). Maybe
thats causing your trouble.

Kind Regards,

Thomas

> 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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> AMBER_at_ambermd.org
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>

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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