From: James Starlight (jmsstarlight_at_gmail.com)
Date: Fri Jun 28 2013 - 15:28:40 CDT
Dear NAMD users!
I'm simulating my water soluble protein in NPT ensemble using Langevens
dynamics.
According to the NAMD tutorial I've noticed that values for the dampling
coefficent as well as langevinPistonPeriod should I specify manually in
accordance to my system.
1) I've noticed that during simulations in the NVT ensemble damping
coefficient typically slightly bigger than in npt simulation. Should I use
bigger dampling in equilibration period (weaker coupling to the temperature
bath) ?
2) On what assumptions should I chose reasonable langevinPistonPeriod as
well as langevinPistonDecay in the equilibration and production runs?
3) What differences in the temperature-pressure parameters should be
introduced with membrane protein simulation?
Thanks for help,
James
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