AMBER Archive (2008)

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

From: Majeed Shaik (m.shaik_at_manchester.ac.uk)
Date: Wed Sep 10 2008 - 12:42:58 CDT

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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