Dear all,
When i was reading the manual for temperature regulation, i saw a
statement: "Since Langevin simulations are potentially susceptible to
"synchronization" artifacts, you should explicitly set the ig variable
(described below) to a different value at each restart of a given
simulation."
I check amber mailing list for this ig value as well...and in one of
the tutorial (Loop Dynamics of the HIV-1 Integrase Core Domain) ig
value was used.
If i want to use ntt=3 and run the 1.8 ns of simulation by 9x200ps
run, as shown by amber workshop tutorial-A Practical Example (A-DNA),
do i need to set ig value? Because the tutorial does not set this ig
value.
in short, all simulations that use ntt=3, regardless the system size
and nature, will need to set ig value? same for sander and pmemd?
Thanks and regards,
Colvin
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Received on Fri Sep 03 2010 - 01:00:04 PDT
