Hi Jason,
Thanks for the answer. Since degrees of freedom will also be counted for restrained atoms, in the equilibration procedure intended to equilibrated the solvents only, will performing Langevin dynamics with a very strong restraint on protein atoms (e.g. 500 kcal/(mol*A^2)) towards the initial configuration cause any danger? Like the protein atoms are strongly restrained (hence very small velocities) but they will be still counted when calculate the temperature, which would cause the solvents move faster than they should be towards the target temperature.
Kind regards,
Pengfei
> On Apr 4, 2017, at 12:24 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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 Wed Apr 05 2017 - 15:30:03 PDT
