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
