AMBER Archive (2005)

Subject: AMBER: TI calculation using sander

From: Latifa Douali (latifa.douali_at_pnl.gov)
Date: Tue Jun 07 2005 - 19:10:54 CDT

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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