hrm, just noticed the previous posts about this problems with TIP4, box
sizes, etc.. Perhaps that is the problem.
I'll try a larger octahedron and see what happens.
Sorry for the in-box pollution.
Andrew
Andrew Borgert wrote:
> Using AMBER9 on an intel linux workstation, I am running MD on a very small
> glycopeptide with explicit solvent, and I got the following error part way
> through the run:
>
>
>
> Cutoff list exceeds largest sphere in unit cell!!
> Big problems with imaging!!
> a,b,c = 29.3936780883931 29.3936780883931
> 29.3936780883931
> alpha,beta,gamma = 109.471219000000 109.471219000000
> 109.471219000000
> cutlist,sphere = 12.0000000000000 11.9999194351816
>
>
> The MD run has the following parameters which I have used before without
> problem:
> &cntrl
> imin=0,
> irest = 1,
> ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
> cut = 10,
> ntr = 0,
> ntc = 2,
> ntf = 2,
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 100000, dt = 0.001,
> ntpr = 200, ntwx = 200, ntwr = 200
> /
>
> The system was setup in xLeap, and water added using the following command:
>
> solvateoct m TIP3PBOX 9.0
>
> Any suggestions?
>
>
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Received on Sun Jul 15 2007 - 06:07:41 PDT
