Re: Improve scaling for large amount of fixed atoms

From: Tristan Croll (
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.

Tristan Croll
Faculty of Science and Technology
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443

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On 19 Mar 2014, at 6:40 pm, "Norman Geist" <<>> wrote:

Hi experts,

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.

Any ideas?

Thanks in advance


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