AMBER: Cutoff list exceeds largest sphere in unit cell

From: Majeed Shaik <m.shaik.manchester.ac.uk>
Date: Wed, 10 Sep 2008 15:54:58 +0100

 

Using AMBER9 I am running a MD simulations of 32 imidazole molecules in 216
TIP3P water molecules and the following is the input

 

Imidazole : 250ps MD

 &cntrl

  imin = 0,

  irest = 1,

  iwrap = 1,

  ntx = 5,

  ntb = 2,

  pres0 = 1.0,

  ntp = 1,

  taup = 2.0,

  cut = 8,

  ntr = 0,

  ntc = 2,

  ntf = 2,

  tempi = 298.0,

  temp0 = 298.0,

  ntt = 1,

  nstlim = 500000,

  dt = 0.0005,

  ntpr = 10000,

  ntwx = 50000,

  ntwr = 10000

  /

And the put the TIP3P molecules using solvatebox TIP3PBOX 6.2

 

I get the following error from the simulation

 

 

---------------------------------------------------------------------------- 
----
   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
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST =      27841
| TOTAL SIZE OF NONBOND LIST =     123196
check COM velocity, temp:        0.000000     0.00(Removed)
check COM velocity, temp:        0.000000     0.00(Removed)
check COM velocity, temp:        0.000000     0.00(Removed)
check COM velocity, temp:        0.000000     0.00(Removed)
 Cutoff list exceeds largest sphere in unit cell!!
 Big problems with imaging!!
 a,b,c =    34.9189665530652        34.1192964048493
   19.9999946872118
 alpha,beta,gamma =    90.0000000000000        90.0000000000000
   90.0000000000000
 cutlist,sphere =    10.0000000000000        9.99999734360589
 
 
any suggestions please.
 
Thank you 
 
Majeed
 
 
 
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Received on Thu Sep 11 2008 - 08:41:35 PDT
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