Hello Ross,
I forgot to mention I have used the command setbox before using solvatebox.
Majeed
_____
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Ross Walker
Sent: 10 September 2008 17:01
To: amber.scripps.edu
Subject: RE: AMBER: Cutoff list exceeds largest sphere in unit cell
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
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Received on Thu Sep 11 2008 - 08:42:05 PDT
