On Sat, Apr 15, 2017, Thomas Charles Pochapsky wrote:
> I am running a constant pressure equilibration of a solvated protein in
> Sander, the run truncated with the following message:
> /In this slab, Atoms found: 6578 Allocated: 5629//
> //
> //***** Processor 18//
> //***** System must be very inhomogeneous.//
> //***** Readjusting recip sizes.//
Run your initial pressure simulation in serial mode, or with a small number
of threads for sander. (Or, use pmemd if you have that available.) Once
you obtain a good density, you can switch back to using a larger number of
threads.
> cut=16,
This is almost certainly a big waste of effort for equilibration. Consider
using the default value of 8.
There might be something else going on, but try these suggestions first.
....dac
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Received on Mon Apr 17 2017 - 05:00:02 PDT
