[AMBER] Total system charge and TI simulations

From: Veenis, Andrew Jay <ajv6.psu.edu>
Date: Mon, 1 Oct 2018 19:29:05 +0000


I would like to use TI to obtain pKa estimates of functional groups in RNA molecules. Water and ions will be modeled explicitly and the systems will typically consist of ~30,000 atoms. Because the functional group will be neutral at = 0 and charged at = 1, the overall system will also be neutral and charged, respectively. From what I have read, this should be okay as long as the system is sufficiently large, however, this is based on literature/discussion from 10+ years ago. Several suggestions were provided in an older post, found at http://archive.ambermd.org/200708/0288.html. Is there now a preferred way of handling these types of simulations? Is it best to just let the charge of the total system change or should I implement something to keep the system neutral?


Drew Veenis

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Received on Mon Oct 01 2018 - 12:30:02 PDT
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