I'm running a minimisation using amber11.
In amber11_serial there's seems to be no problem.
Yet running the same input files on a 16 processor machine, I get the error message below.
Any ideas about this?
Many thanks
George
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 08/20/2010 at 14:20:31
[-O]verwriting output
File Assignments:
| MDIN: min.in
| MDOUT: min.out
|INPCRD: 1dqe_bom_solv.inpcrd
| PARM: 1dqe_bom_solv.prmtop
|RESTRT: min.rst
| REFC: 1dqe_bom_solv.inpcrd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
minimise 1dqe-bom
&cntrl
imin=1,maxcyc=1000,ncyc=500,
cut=8.0,ntb=1,
ntc=2,ntf=2,
ntpr=100,
ntr=1, restraintmask=':1-138',
restraint_wt=2.0
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
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 = 31.547
| New format PARM file being parsed.
| Version = 1.000 Date = 08/18/10 Time = 18:51:43
NATOM = 23972 NTYPES = 17 NBONH = 22878 MBONA = 1109
NTHETH = 2439 MTHETA = 1489 NPHIH = 4602 MPHIA = 3712
NHPARM = 0 NPARM = 0 NNB = 40936 NRES = 7418
NBONA = 1109 NTHETA = 1489 NPHIA = 3712 NUMBND = 52
NUMANG = 103 NPTRA = 45 NATYP = 37 NPHB = 1
IFBOX = 1 NMXRS = 47 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 1691445
| Hollerith 79336
| Integer 949042
| Max Pairs 665888
| nblistReal 287664
| nblist Int 998857
| Total 25981 kbytes
| Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 1, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Energy minimization:
maxcyc = 1000, ncyc = 500, ntmin = 1
dx0 = 0.01000, drms = 0.00010
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 69.814 Box Y = 69.707 Box Z = 63.093
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 72 NFFT2 = 72 NFFT3 = 64
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
Mask :1-138; matches 2146 atoms
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 7273
| Atom division among processors:
| 0 1499 2996 4496 5993 7490 8990 10487
| 11984 13484 14981 16478 17978 19475 20972 22472
| 23972
Sum of charges from parm topology file = -0.99800005
Assuming uniform neutralizing plasma
| Running AMBER/MPI version on 16 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
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Received on Fri Aug 20 2010 - 07:00:03 PDT
