AMBER Archive (2006)

Subject: AMBER: PCA results with explicit Vs Implicit solvation

From: Keerthi Gottipati (
Date: Mon Nov 06 2006 - 10:32:16 CST

Hi all,

I would like to know how(if at all) a choice of solvation method (i.e.
implicit vs explicit) would reflect on the final analysis of a peptide
(115 residue) if I'm using PCA to extract any conspicuous domain
motions. I've analysed the trajectory from a GB simulation(1ns) and
wondering if the overall behaviour would be any different with explicit
solvent conditions.

Thanks in advance,
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