Hi Jason:
thank you very much for kind reply.
I see the problem. I simple add the periodic information at the end
of my prmtop file..... since I don't find how to add periodic
information to the system from Amber online tutorial or manual..... Did
you have any idea have to generate periodic information in Amber?
thank you very much
best
Albert
On 05/09/2012 09:26 PM, Jason Swails wrote:
> On Wed, May 9, 2012 at 3:07 PM, Albert<mailmd2011.gmail.com> wrote:
>
>> Dear:
>>
>> I am using the following input file for a simulations, but it failed:
>>
>> equilibration
>> &cntrl
>> imin=0, irest=1, ntx=5,
>> nstlim=1000000, dt=0.002,
>> ntc=2, ntf=2,
>> cut=10.0, ntb=2, ntp=3, taup=2.0,
>> ntpr=5000, ntwx=5000, ntwr=50000,
>> ntt=1,
>> temp0=310.0,
>> csurften=3, gamma_ten=60, ninterface=2,
>> restraintmask=':PE:1-311& !.H=',
>> restraint_wt=50.0
>> /
>>
>>
>> --------------log--------------------------
>>
>> | PMEMD ewald parallel performance parameters:
>> | block_fft = 0
>> | fft_blk_y_divisor = 2
>> | excl_recip = 0
>> | excl_master = 0
>> | atm_redist_freq = 320
>> | ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported!
>>
> You are trying to do a NTP simulation with periodic boundary conditions,
> but your prmtop is not set up for periodic simulations.
>
> HTH,
> Jason
>
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Received on Wed May 09 2012 - 13:00:04 PDT
