[AMBER] Doubt regarding Collision frequency during NEB simulations

From: SHAUNAK BADANI <shaunak.badani.research.iiit.ac.in>
Date: Fri, 31 Jan 2020 19:37:03 +0000

Dear Amber users,

I am a beginner and I want to run NEB simulations on a protein system in explicit solvent, using simulated annealing protocol.

I read about collision frequency (gamma_ln) in the Amber18 manual and on NEB tutorial. But, the effect of implicit/explicit solvent model on the value of gamma_ln is still not clear to me. Also, I am not sure whether there is a relation between gamma_ln related and the spring constant used during neb simulations.

Any help in this regard would be much appreciated.

Shaunak Badani
IIIT Hyderabad

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Received on Fri Jan 31 2020 - 12:00:02 PST
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