AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Sep 10 2008 - 15:08:53 CDT

Hi Majeed,

 

Sorry for the misunderstanding, I just assumed by the fact that you had so
few waters that this must be a solvent cap simulations. In this case you
have a very small number of water molecules for a periodic simulation. A 6.2
angstrom buffer of water for the solvatebox command is very small and I
suspect that your box is rapidly shrinking, due to the initial density being
too low and then the box is too small for the cutoff. AMBER was never
designed to simulate very small periodic systems. I suggest adding much more
water to your system, at a minimum in this situation I would suggest adding
a 10 angstrom buffer of water although even this may be too small once the
density equilibrates. Try printing to the output more frequently so you can
see how the box volume reduces during the simulation before it stops. (do
NOT set the cut off less than 8 angstroms).

 

Good luck,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Majeed Shaik
Sent: Wednesday, September 10, 2008 10:43 AM
To: amber_at_scripps.edu
Subject: RE: AMBER: Cutoff list exceeds largest sphere in unit cell

 

Hello Ross,

 

I am infact trying to run a simulation with periodic conditions … in my
system with a particular conc. Hence I have 32 imidazoles with 216 waters. I
am not sure if I am right using solvatebox TIP3PBOX command to do in such
way. If I am wrong whats the right way to do it…

 

I have 0.5fs arbitrarily ….

 

Majeed

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Ross Walker
Sent: 10 September 2008 17:01
To: amber_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Majeed Shaik
Sent: Wednesday, September 10, 2008 7:55 AM
To: amber_at_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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