On Mon, Sep 14, 2015, Huggins, Esther, C wrote:
>
> I'm trying to resolve some issues with the minimization ...
>
>
> Heating of 1M NaNO3 STAGE 1
> &cntrl
> imin=0, irest=0, ntx=1,
> nstlim=4000000, dt=0.0005,
> cut=4.0,
Ouch....you can't use such a short cutoff! Use the default value of 8.
You should be able to use a dt value of 0.001 or 0.002, once you start getting
a stable simulation.
> ntf=2,ntc=2,
> ntt=3, gamma_ln=1.0,
> tempi=0.0, temp0=100.0,
> ntpr=50, ntwx=50,
> ntb=1,
> iwrap=1, ipol=1, ig=-1
If you are new to Amber, use a non-polarizable potential first (ipol=0).
Equilibrate the system with non-polarizable potentials, then you try
polarizable ones.
Carry out trial runs with ntpr=1, nstlim=100; use just the serial version
(not the parallel version). It looks like your starting coordinates for
MD have not been minimized (or minimized enough).
....good luck....dac
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Received on Sun Sep 13 2015 - 21:30:04 PDT
