On Tue, Apr 4, 2017 at 1:14 PM, pengfei li <ldsoar1990.gmail.com> wrote:
> Thank you very much for who have replied. I have another quick question:
> when AMBER calculates the temperature of a system which has atoms frozen or
> restrained, does these frozen or restrained atoms are still counted? Thanks!
>
Be careful with your terminology. Restrained and constrained are two
different conditions. Restrained degrees of freedom oscillate around some
fixed reference. Constrained degrees of freedom do not, and are
"frozen". This is the critical difference between constraints and
restraints.
The temperature of a system is computed using its degrees of freedom.
Constraints lower the number of degrees of freedom (and thus are omitted
when calculating the temperature). Common constraints in Amber are those
added between hydrogen-heavy atom bonds (those constraints are solved using
SHAKE or SETTLE), and "frozen" atoms using the "ibelly" keyword.
Restraints do not reduce the number of degrees of freedom (but they also
permit motion along those restrained coordinates, so they contribute to the
total kinetic energy).
I hope this answers your question.
All the best,
Jason
--
Jason M. Swails
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Received on Tue Apr 04 2017 - 10:30:02 PDT
