Hello
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
If anybody can shortout my problem then help me.
Thanks
Sangita Kachhap
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Received on Wed Jan 20 2010 - 01:30:03 PST
