AMBER Archive (2007)

Subject: AMBER: sander and pmemd

From: Nadia Vahdati (nadiav_at_soton.ac.uk)
Date: Mon Dec 03 2007 - 07:20:17 CST

Dear Amber users,

I am simulating a solvated protein system ~65000 atoms.

I usually minimise with a serial version of sander-9. In the equilibration
stage and production, I then switch to a parallel version and use around 16
processors.

I now have access to a parallel version of PMEMD-9 with large number of
processors to use.

- I understand that pmemd is a reimplementation and should replicate sander
but with much better speed of performance. Is it ok to mix sander and
pmemd? ie. use sander for the minimisation and
heating and then pmemd for production?

-or should I only use pmemd? and just reduce the number processors used
during the minimisaiton and heating?

Thank you in advance for any advice,

Nadia 

--
Nadia Vahdati
Postgraduate Research Student
Prof. J.W. Essex Group
University of Southampton
UK.

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