From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Mar 19 2014 - 21:15:40 CDT
I would suggest looking at the AutoIMD code to see how it breaks out a subset of your structure for simulation then writes the coordinates back to the original PSF/PDB when finished. No sense holding the whole thing in memory at all if it's mostly fixed.
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On 19 Mar 2014, at 6:40 pm, "Norman Geist" <norman.geist_at_uni-greifswald.de<mailto:norman.geist_at_uni-greifswald.de>> wrote:
is there any way currently, to influence the parallel departing of the simulation cell? Iím asking because Iím currently using a system where almost everything is fixed (a huge protein where we only try to fold a C-TERM onto it). So NAMD does of course depart the work equally to all processors and we do not get any speed gain throughout the fixing. PME is turned off of course.
Thanks in advance
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