Hi David. I'll take your suggestion and equilibrate the system at a lower
processor count to see if that changes. I think you have a very good point
there.
The error indeed comes right before the information about the first step is
printed.
Regarding the scmask, I've already done a simulation decoupling :342
entirely. Res 342 is a water molecule. The idea is to calculate the pka
shift for this molecule relative to a few point mutations in the active
site. I am running this :342.H2 out of curiosity. I want to see if the
shifts are still the same (or at least close to the ones I had for scmask =
:342). I didn't encounter the error before because I had never used more
than 8 processors at a time.
Thanks
Fabrício
2013/9/18 David A Case <case.biomaps.rutgers.edu>
> On Wed, Sep 18, 2013, Fabrício Bracht wrote:
>
> > Hello. I am using amber12 (fully patched) to perform TI calculations. I
> am
> > having somoe problems related to the number of processors used for the
> > calculation. Everytime I choose set -np bigger than 8, the calculation
> > starts with the warning:
> >
> > ***** Processor 0
> > ***** System must be very inhomogeneous.
> > ***** Readjusting recip sizes.
> > In this slab, Atoms found: 6266 Allocated: 6094
>
> Is your system well equilibrated (at this lambda)? If not, try running
> some equilibration at a lower processor count, and see if that helps.
>
> Also, have you done simulation with a very small number of steps and
> ntpr=1?
> It is useful to know if the error message comes at the very first step or
> not.
>
>
> > icfe = 1, ifsc = 1, clambda = 0.02544,
> > noshakemask = ':342', scmask = ':342.H2', idecomp = 1, nmropt = 0,
>
> This is pretty unusual: do you really want to decouple just a single
> hydrogen
> atom? Also, do you see problems at larger values of clambda?
>
> ...dac
>
>
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Received on Wed Sep 18 2013 - 14:00:02 PDT
