Hi all,
I am trying to redo the TI example given in the tutorial of amber8. I
run the job as described in the tutorial. Sudenly, the calculation
crashed with this error message:
> unreasonably small cut for non-periodic run: 8.00
>
> *** input error(s)
My output file looks like:
Here is the input file:
neutralize toluene
&cntrl
ntr=0,
nstlim = 100000, nscm = 2000, ntave = 10000,
ntx =5, irest=1, ntb=0, ntpr=200,
dt=0.001, nrespa=2,
ntt=1, temp0=300., tautp=2.0,
ntc=2, ntf=2, tol=0.000001,
ntwr = 10000, ntwx=0,
icfe=1, clambda=0.5,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| *** cutoff > system size, list only builds once
|Largest sphere to fit in unit cell has radius = 31.913
| New format PARM file being parsed.
| Version = 1.000 Date = 06/07/05 Time = 10:37:12
NATOM = 15 NTYPES = 4 NBONH = 8 MBONA = 7
NTHETH = 16 MTHETA = 8 NPHIH = 27 MPHIA = 9
NHPARM = 0 NPARM = 0 NNB = 68 NRES = 1
NBONA = 7 NTHETA = 8 NPHIA = 9 NUMBND = 4
NUMANG = 5 NPTRA = 3 NATYP = 4 NPHB = 0
IFBOX = 0 NMXRS = 15 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 2216
| Hollerith 93
| Integer 388287
| Max Pairs 105
| Max Rstack 50195
| Max Istack 75
| Total 1927 kbytes
Running a free energy calculation with lambda = 0.500
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
PHE
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 200, ntrx = 1, ntwr
= 10000
iwrap = 0, ntwx = 0, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 2, ntb = 0, igb = 0, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 100000, nscm = 2000, nrespa = 2
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 0.00000, tautp = 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00000
Free energy options:
klambda = 1
clambda = 0.50000
unreasonably small cut for non-periodic run: 8.00
*** input error(s)
--------------------------------------------------------
Thank you for your help
Latifa
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Received on Wed Jun 08 2005 - 01:53:01 PDT
