Hi
The constant pH algorithm in amber consists of two parts. In the first
one, regular MD is performed with a certain set of protonation states.
The charge of the system is then treated like in any other regular MD
run, using PME. If there is extra charge, it is dealt with a
neutralizing plasma, again, like in any MD in amber.
The second part is a montecarlo step to see if one can change
protonation state. This MC is done in implicit solvent, using GB with an
infinite cutoff, so there are no issues about charges there either.
adrian
On 8/29/22 9:58 AM, Dulal Mondal via AMBER wrote:
> [External Email]
>
> Dear Users,
>
> I am running CpHMD simulation. Can you help me how the charge of the system
> is maintained and how the long range electrostatics of the system is taken
> care of?
> with regards,
> Dulal Mondal
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--
Dr. Adrian E. Roitberg (he/him/el)
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Aug 29 2022 - 13:30:03 PDT
