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Dr. Michael Jakusch
ETH - Swiss Federal Institute of Technology
Departement of Applied Biosciences
Winterthurerstrasse 190
CH-8057 Zürich
Switzerland
Phone: +41.1.635 60 71
Fax: +41.1.635 68 84
email: michael.jakusch_at_pharma.anbi.ethz.ch
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Header of MDOUT
*****************************************************************
-------------------------------------------------------
Amber 6 SANDER Scripps/UCSF 1999
-------------------------------------------------------
| Thu Sep 6 18:20:26 2001
File Assignments:
|MDIN : _sandin_
|MDOUT: tko_npt1.out
|INPCR: tko_nvt2.crd
|PARM : tk_apo_oct.prmtop
|RESTR: tko_npt1.crd
|REFC : refc
|MDVEL: mdvel
|MDEN : tko_npt1.mden
|MDCRD: tko_npt1.mdcrd
|MDINF: mdinfo
Here is the input file:
#L1
#L2
#L2
&cntrl
imin=0,
ntx=7
nstlim=50000,dt=.002
ntpr=10,ntwe=10,ntwx=100
ntc=2,ntf=2,tol=0.00001
ntb=2, cut=9, scee=1.2
ntt=1, tautp=.2
ntp=1, taup=.05
temp0=300
ibelly=0
&end
-------------------------------------------------------------------------------
#L1
1. RESOURCE USE:
getting box info from bottom of parm
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
EWALD SPECIFIC INPUT:
-------------------------------------------------
NO EWALD INPUT FOUND: USING DEFAULTS
-------------------------------------------------
Largest sphere to fit in unit cell has radius = 46.261
Calculating ew_coeff from dsum_tol,cutoff
Box X = 105.242 Box Y = 96.666 Box Z = 92.522
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 108 NFFT2 = 96 NFFT3 = 96
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
NATOM = 39522 NTYPES = 17 NBONH = 34484 MBONA = 5150
NTHETH = 11434 MTHETA = 7042 NPHIH = 21356 MPHIA = 13262
NHPARM = 0 NPARM = 0 NNB = 94936 NRES = 10488
NBONA = 5150 NTHETA = 7042 NPHIA = 13262 NUMBND = 43
NUMANG = 87 NPTRA = 39 NATYP = 31 NPHB = 1
IFBOX = 2 NMXRS = 24 IFCAP = 0
EWALD MEMORY USE:
| Total heap storage needed = 1641
| Adjacent nonbond minimum mask = 94936
| Max number of pointers = 25
| List build maxmask = 189872
| Maximage = 57820
EWALD LOCMEM POINTER OFFSETS
| Real memory needed by PME = 1641
| Size of EEDTABLE = 20768
| Real memory needed by EEDTABLE = 83072
| Integer memory needed by ADJ = 189872
| Integer memory used by local nonb= 2635590
| Real memory used by local nonb = 647724
| MAX NONBOND PAIRS = 40000000
| Memory Use Allocated Used
| Real 20000000 2274558
| Hollerith 4800000 247622
| Integer 80000000 4342895
| Max Nonbonded Pairs:40000000
BOX TYPE: TRUNCATED OCTAHEDRON
2. CONTROL DATA FOR THE RUN
TIMLIM= 999999. IREST = 0 IBELLY= 0
IMIN = 0
IPOL = 0
NTX = 7 NTXO = 1
IG = 71277 TEMPI = 0.00 HEAT = 0.000
NTB = 2 BOXX = 105.242
BOXY = 96.666 BOXZ = 92.522
NTT = 1 TEMP0 = 300.000
DTEMP = 0.000 TAUTP = 0.200
VLIMIT= 0.000
NTP = 1 PRES0 = 1.000 COMP = 44.600
TAUP = 0.050 NPSCAL= 0
NTCM = 0 NSCM = 9999999
NSTLIM=50000 NTU = 1
T = 0.000 DT = 0.00200
NTC = 2 TOL = 0.00001 JFASTW = 0
NTF = 2 NSNB = 25
CUT = 9.000 SCNB = 2.000
SCEE = 1.200 DIELC = 1.000
NTPR = 10 NTWR = 50 NTWX = 100
NTWV = 0 NTWE = 10 IOUTFM= 0
NTWPRT= 0 NTWPR0= 0 NTAVE= 0
NTR = 0 NTRX = 1
TAUR = 0.00000 NMROPT= 0 PENCUT= 0.10000
IVCAP = 0 MATCAP= 0 FCAP = 1.500
OTHER DATA:
IFCAP = 0 NATCAP= 0 CUTCAP= 0.000
XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000
VRAND= 0
NATOM = 39522 NRES = 10488
Water definition for fast triangulated model:
Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2
3. ATOMIC COORDINATES AND VELOCITIES
Largest sphere to fit in unit cell has radius = 46.261
NEW EWALD BOX PARAMETERS from inpcrd file:
A = 105.24217 B = 96.66571 C = 92.52201
ALPHA = 90.00000 BETA = 90.00000 GAMMA = 90.00000
begin time read from input coords = 6.500 ps
Number of triangulated 3-point waters found: 9814
Sum of charges from parm topology file = -0.00000028
Forcing neutrality...
---------------------------------------------------
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 = 0.3302E-14 at 2.581700
| CHECK d/dx switch(x): max rel err = 0.8064E-11 at 2.761360
---------------------------------------------------
Total number of mask terms = 84636
Total number of mask terms = 169272
| Total Ewald setup time = 0.15999985
------------------------------------------------------------------------------
Received on Fri Sep 07 2001 - 06:24:53 PDT