From: ARTURAS ZIEMYS (ziemys.1_at_osu.edu)
Date: Wed Mar 01 2006 - 09:30:20 CST
How NAMD deals with system containing different compounds with different compressabilities, e.g.: water (isotropic) and protein (anisotropic) ?
Please, let me know if I am correct (I am not a physicist...):
1. During pressure increase, all space is scaled equally (be protein or water) and box size is adjusted.
2. Because of different components in my system I have different "local" (say at direction x,y,z,...) pressures right after my system was rescaled.
- Is it useful or needed to turn-on the "useFlexibleCell" at pressure
increase for systems like is described above ?
3. Some time is required to "restore" right structures to certain pressure, because protein and water have different properties.
- What is the general times of equilibration after pressure change ?
Thank you for patients and answers
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