[AMBER] gbsa parameter

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Wed, 3 Aug 2016 17:54:11 +0200


The 'gbsa' parameter is set to 0 by default and when I set it to 1 or 2,
the GB simulations as slowed down. Is the SASA calculation necessary,
namely have the igb=1, 2, 5, 7 or 8 been optimized using gbsa=0 or not?

Another question. OpenMM calculates by default the SASA using the "ACE
approximation". Should I turn this feature off to get consistent results
when I run GB simulations with AMBER .prmtop files (provided I used option
gbsa=0 in AMBER simulations)?

​thanks in advance

Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Aug 03 2016 - 09:00:02 PDT
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