RE: AMBER: Cutoff list exceeds largest sphere in unit cell

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 10 Sep 2008 09:01:18 -0700

Hi Majeed,

 

You have set up a solvent cap system (in a sphere of water) but are trying
to run a periodic simulation (ntb=2, ntp=1) - hence the problems.

 

Are you sure that a non-periodic harmonic boundary solvent cap is what you
want to run? You should be using a cut off with this type of simulation btw
(set cut = 999) which will likely mean it is slower than a periodic boundary
simulation - hence you would probably be better off running a full periodic
simulation, unless there is some reason for running the solvent cap.

 

Do you also have a reason for using a 0.5fs time step with shake on?

 

Good luck,

Ross

 

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Majeed Shaik
Sent: Wednesday, September 10, 2008 7:55 AM
To: amber.scripps.edu
Subject: AMBER: Cutoff list exceeds largest sphere in unit cell

 

 

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
 
 
 
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo.scripps.edu
Received on Thu Sep 11 2008 - 08:41:46 PDT
Custom Search