AMBER Archive (2006)

Subject: AMBER: How to find equillibration time for my system in a generalised born solvation model

From: Gobind Singh Bisht (gsbisht1_at_gmail.com)
Date: Mon Oct 16 2006 - 16:34:11 CDT

Dear all,
          I have a 42 bp DNA implicitly solvated with generalised born
solvation model ( igb=1) using the Langevin thermostat... I want to study
the system under changing temperature conditions. How do i find the minimum
time required for equilibration of my system before i can get a production
MD trajectory and the system is ready for a second phase of temperature
change and so on.. Is there any order of magnitude calculation that can be
done to find the equilibartion time??... another question is how exactly is
the thermostat coupled to the GB solvation scheme... can anyone refer some
papers to me where i can get a look at the analytical equations for this
implementation?? Also Langevin Dynamics implementation as such has a viscous
term associated to it whereas in implicit solvation there is no viscosity
(atleast that is mentioned in the tutorials or i could figure out from the
eqns).. so how does Langevin thermostat exactly work with implicit
solvation, in specific, GBS model... Please bear with me if any question is
very basic but i'm still in the stage of exploring MD and AMBER.
thanx in advance

gobind

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