Folding@home AMBER FAQ

Table of Contents

The Folding@home (FAH) developers (primarily Jim Caldwell and Young Min Rhee) have been working with the AMBER development team (of which Jim Caldwell is a long time member) to incorporate AMBER into Folding@home.

As a participant of Folding@home, is there anything I need to do?

No. For the participants of Folding@home, nothing new needs to be done, the update is automatic.

Why include AMBER? What do you gain?

For the scientists using Folding@home, the results will be dramatic. For GB/SA calculations (see the AMBER GB page for details), AMBER affords benefits over the current GB/SA code in Folding@home (the current code is based on Jay Ponder's Tinker), especially a great speed increase (perhaps up to 5x). This will substantially increase the power of Folding@home for many calculations. Also, AMBER adds not just speed, but new functionality in its ability to perform polarizable force field calculations (which cannot be performed with Gromacs or our current Tinker 3.8 implementation).

If it's faster, will the participants get more points?

Sorry, the points in the stats will still be benchmarked by the CPU time, so your stats will not be affected.

How can AMBER be that much faster?

AMBER's GB/SA code is more recently written and more heavily optimized than Tinker. Gromacs does not have GB/SA functionality.

What about SSE/3D-Now/Altivec support?

Currently, SSE and SSE2 are not supported. AMBER is run in double precision so SSE would not help. SSE2 could help, but would not provide a significant speed increase. Our first goal was to get AMBER running stably and we will then try to further tweak optimizations with SSE2. However, we expect to gain only 10% speed increase.

What about Mac OS X support?

We will be adding OS X support once the Win and Lin ports settle down. We are currently looking into what would be the best FORTRAN 90 compiler for OS X.

Why didn't you use AMBER earlier?

AMBER has just been recently rewritten in FORTRAN90 which makes it more friendly for Windows compilation. Also, Jim Caldwell (long time AMBER developer) has just recently joined the FAH team.

Has the current scientific code been slowing you down unnecessarily?

No: since AMBER's fast GB/SA code is itself pretty new to AMBER, there hasn't been a significant speed advantage, until recently.

What about the current scientific codes? What will happen to them?

We will continue to perform most calculations with Gromacs. However, we expect that AMBER will take over for many of the calculations which we would start on Tinker.

Is there a charge for using AMBER?

FAH has permission (from Dave Case at Scripps) to run AMBER on the FAH supercomputer and no FAH donators will have to pay any sort of AMBER fee. However, if someone wants to use AMBER for their own research (i.e. not for running FAH, but for some other purpose), then there would be a fee. The AMBER core in FAH has been designed to run only FAH calculations and the FAH AMBER core cannot be used for any other purpose.

What modifications will you be making to AMBER, and when will they be available?

Essentially all of our AMBER modifications are involved with connecting AMBER to FAH. We will make these available to AMBER developers, but likely they will not include them in the AMBER distribution.

I'd like to learn more about AMBER. Where should I look?

First, check out the AMBER web page. Also, a good general overview of the Amber codes can be found in: D.A. Pearlman, D.A. Case, J.W. Caldwell, W.R. Ross, T.E. Cheatham, III, S. DeBolt, D. Ferguson, G. Seibel and P. Kollman. AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules. Comp. Phys. Commun. 91, 1-41 (1995). An overview of the Amber protein force fields, and how they were developed, can be found in: J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv. Prot. Chem. 66, 27-85 (2003). Similar information for nucleic acids is given by T.E. Cheatham, III and M.A. Young. Molecular dynamics simulation of nucleic acids: Successes, limitations and promise. Biopolymers 56, 232-256 (2001).

For More Information, Please See:

• FAH FAQ
• AMBER web page
• Folding Community Forum
• FAH WIKI: FAH CORES

Last Updated on January 24, 2008, at 06:23 AM