Thanks, Dave. I'll try those. Does the periodic box size get reset
automatically to maintain uniform solvent density?
Tom
On 4/17/17 7:43 AM, David Case wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 17 2017 - 07:00:02 PDT
