From: Ryan Gordon (rg563_at_drexel.edu)
Date: Thu Feb 05 2015 - 10:00:28 CST
I was wondering if there was a way to specify what you want the patch grid dimensions to be? I am running a NPT system of roughly 110,000 atoms, and I allow this to run at a temperature close to the solvent boiling point for 100 ns. I then quenched the system at three different time points from this simulation to room temperature. The way I did this was to decrease the temperature by 10K for 100 ps (enough time for the volume to equilibrate), until I reached my desired temperature (293K). When I run at 300K and up the box size is big enough to run on a patch grid of 8 by 8 by 8. When I reduce to 293K, the box size shrinks just enough to run on 7 by 7 by 7 patch grid, which causes a performance hit since there are more atoms per patch now. My first theory is to make the system slightly larger to keep the system in the 8 by 8 by 8 patch grid dimension, to optimize the computational time to complete this. This seemed tedious if there was a way to manually adjust the patch grid dimensions.
Ryan GordonPh.D. Candidate
Chemical and Biological Engineering
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