[modeller_usage] Re: my automodel run well serial, but molpdf is inmediatly exceeded when run in parallel

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 4/7/24 6:47 AM, Mario Bianchet via modeller_usage wrote:
> The script below exceeds molpdf limits immediately when run this
> automodel job on parallel, but run starts with a  low molpdf and ends
> well when commenting the line "a.use_parallel_job(j)" Any hint of how
> to solve will be appreciate?

The model building procedure is the same for both serial and parallel 
jobs; however, parallel jobs run in a slightly different environment (a 
separate process, with the random number generator in a different 
state). So you should not expect to get exactly the same models.

There is always a possibility when building models that the randomized 
starting coordinates are such that the optimizer cannot recover (e.g. a 
knot in the backbone, or atoms placed on top of each other) and in some 
cases this will trigger the max_molpdf cutoff. The solution is the same 
though for both serial and parallel jobs - build multiple models and 
discard the bad ones.

	Ben Webb, Modeller Caretaker
-- 
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