From: Victor Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Sun Aug 19 2007 - 15:21:22 CDT
I my NVE simulations of a solvated protein system done at 298K (about
110,000 atoms), the temperature increases by 4 degrees over 12 ns; K.E.
increases by 700 kcal/mol; total energy increases by 2200 kcal/mol;
a snippet from my script is at the end of this message;
1)The integrator used in NAMD is Verlet, which is energy conservative,
2)How is the total energy expected to vary in practice?
3)Is conservation affected by rattle/shake,
4)Is conservation affected by Timestep splitting?
5) Which of the script parameters could affect stability the most in
this case (dt, stepspercycle, fullElectFrequency) ?
Thanks for any feedback,
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