Hello
Thanks for your suggestion.I applied your suggestion and now i am not getting
such type of problem
> 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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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Thu Jan 21 2010 - 00:00:02 PST
