On Mon, Aug 29, 2022, Dulal Mondal via AMBER wrote:
>
>I am running CpHMD simulation. Can you help me how the charge of the system
>is maintained
Charge is not maintained: it will rise and fall as protons are bound or
unbound from the system.
> and how the long range electrostatics of the system is taken care of?
This depends on what flavor of constant pH simulation you are doing. If
generalized Born is used (which I recommend starting with if you are new to
CpHMD), electrostatic interactions beyond the nonbonded cutoff are ignored.
You should therefore use a large cutoff. It is common practice to set the
cutoff to be much larger than the size of the system -- this effectively
means that there is no cutoff.
For explicit solvent simulations, the particle-mesh Ewald scheme is used to
handle long-range electrostatics. This is a more complex subject than can
be handled in a single email (especially since you may be using GB anyway.)
....dac
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Received on Mon Aug 29 2022 - 13:30:05 PDT
