On Wed, May 9, 2012 at 3:36 PM, Albert <mailmd2011.gmail.com> wrote:
> 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?
>
You can use the "setBox" command in tleap to add periodic box information.
If you add a solvent box, this should be done automatically.
HTH,
Jason
>
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 09 2012 - 13:00:05 PDT
