[AMBER] lambda option in SEBOMD

From: Margarita I. Bernal-Uruchurtu <mabel.uaem.mx>
Date: Mon, 17 Dec 2018 14:15:38 +0100


I've been looking for some further information of how is the lambda option
working with SEBOMD.
This option allows for a smooth transition from a MM simulation of a system
to a SEBOMD (QM) description of it. I know that I have to run several
trajectories using increasing values of lambda to switch to a fully SEBOMD

I've tried to start a simulation using lambda=0.1 and sander does the
number of steps needed, however, there's not a mention of the MM energy in
the output and I'm only getting SEBOMD energy values there. And since the
fluctuations are huge and the temperature rises a lot, I think that it's
not working as stated in the manual.

Am I missing something? How can I make sure that the lambda option is
doing what it's supossed to do?

Thanks in advance,


Science is built with facts as a house is with stones, but a collection of
facts is no more a science than a heap of stones is a house. - Henri
Margarita I. Bernal-Uruchurtu
Centro de Investigaciones Química, UAEM
+52.777.329.7000 ext 6003
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Received on Mon Dec 17 2018 - 05:30:04 PST
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