On Wed, Jan 20, 2010, sangita.imtech.res.in wrote:
> I am simulating cubic water box(TIP3BOX) using amber9 and getting the following
> problem.
> After 31800 step in second molecular dynamics
>
> Cutoff list exceeds largest sphere in unit cell!!
> Big problems with imaging!!
> a,b,c = 30.4619278953131 27.9998611680012
> 30.4338994135927
> alpha,beta,gamma = 90.0000000000000 90.0000000000000
> 90.0000000000000
> cutlist,sphere = 14.0000000000000 13.9999305840002
>
> I am using the following namelist:
>
> First i am relaxing the box :
> imin=1,maxcyc=5000,ntb=1,cut=12
^^^^^^^
>
> Moleculat dynamics 1
> imin=0,nstlim=20000,dt=.001,ntpr=200,ntwx=200,
> ntx=1,ntt=3,gamma_ln=1,cut=12,ntb=1,tempi=0,temp0=300
^^^^^^^^
>
> Molecular dynamics 2
> imin=0, nstlim=50000,dt=.001,irest=1,ntpr=200,ntwx=200,
> ntx=7,ntt=3,gamma_ln=1,ntb=2,ntp=1,pres0=1,taup=2.0,cut=12,tempi=300,temp0=300
^^^^^^
The box size has to be bigger than twice the (cutoff + skinnb). You are
asking for a cutoff of 12, and skinnb by default is 2. So as soon as the
box shrinks enough (as the density increases) so that on side is less
than 28, you will get this error.
There is no reason for you to use such a large cutoff -- leave it at the
default value of 8.
...dac
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Received on Wed Jan 20 2010 - 05:30:02 PST
