AMBER Archive (2003)

Subject: (no subject)

From: Richard Dayton Smith (dicksmit_at_umich.edu)
Date: Wed Jul 09 2003 - 12:23:38 CDT

Hi,

    I am working with a large solvated system, (approximately 50000 atoms),
and I am performing a Free Energy Perturbation Calculation which changes the
system from a net neutral to an overall -1 charge. I would like to use PME to
help speed up the calculation in Gibbs, since the system is so big. I notice
in the AMBER6 manual that using PME in Gibbs is experimental. Has this been
tested, and can PME be used with Gibbs and still produce a reliable result?
Also, if it could be used, could the new PMEMD program be incorporated into a
Gibbs calculation to improve efficiency? Any answers to these questions
would be greatly appreciated.

Thank you,
Richard Smith

Graduate Student
University of Michigan