From: Dong Luo (us917_at_yahoo.com)
Date: Thu Jan 05 2006 - 13:11:19 CST
I'm now running NAMD on several peptides (less than
100 residues) in water box. The whole system is heated
to 580K, running for 0.25ns, then cool down back
slowly to RT, in order to watch the conformation
changes of the peptides. My idea is that the potential
energy part is assumed remaining at RT as I guess the
default parameters in NAMD is adjusted to RT. So the
heating only affects the kinetic part and high
temperature will help the system run out of local
minimums in the energy langscape. Most times, it's
fine to get through all the processes and did see
reasonable results. However, sometimes the system
expanded too much (the volume went to 99999999.9999)
when running in 580K or 560K, and won't go back after
that. I'm wondering what's the highest temperature I
can go with my system? Any comments are welcome.
Yahoo! DSL – Something to write home about.
Just $16.99/mo. or less.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:13 CST