From: Tim Cm (springshades_at_hotmail.com)
Date: Sun Aug 15 2004 - 16:48:42 CDT
I'm running my first simulation using NAMD. It seems like everything is set up so that I should be able to do minimization, bringing up to temperature, and equilibration in one step. The issue that I've run into is that if I do it this way, I don't know how to set the temperature in the Langevin dynamics so that it will change over time and hold at the correct temperature. I doubt it, but is it okay to just set langevinTemp to the final temp at the beginning? It seems like this will cause some inaccuracies while the temperature is being changed at the beginning. My question boils down to: Is it possible to do this in one step, or is it better to just run it in two steps? First minimization/bring up to temperature then second equilibrate. Thanks to anyone who is reading.
........ Tim Connolly ........
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