[AMBER] Question about Simulated Annealing procedure

From: filip fratev <filipfratev.yahoo.com>
Date: Sun, 4 Mar 2012 18:29:13 -0800 (PST)

Hi all,
I need of
probably elementary advice... I wanted to perform a "deep sampling"
on two protein portions (mainly loops) that are involved in protein-protein
interactions (relatively large system 240 000 solvated). I performed fifteen 25
ns-long simulations at 600K and 800K (8 heating at 600K and and 7 at 800K) and then cooled back the systems to 310K
via 100K steps for another 25ns. Can I call this "normal/regular" SA
simulation or it is SA-"like"?

 From: Ross Walker <ross.rosswalker.co.uk>
To: 'AMBER Mailing List' <amber.ambermd.org>
Sent: Thursday, March 1, 2012 11:33 PM
Subject: Re: [AMBER] ABMD in pmemd.cuda in AMBER 12
Hi Aron,

> If I was going to make an attempt to do that migration, are you aware
> of
> any fundamental barriers for putting the NCSU codes on the GPU?  I can
> imagine all kinds of horrible problems, but just wondered if you were
> aware
> of some critical issues, or if it was more a matter of time versus user
> interest at this point.

The issue has until recently been one of funding. Going forward it will be
one of prioritizing based on user interest. The real problem with the NCSU
code is that it was effectively dumped into Sander with no real
documentation, in some cases it duplicates other functionality. It doesn't
use the same namelist approaches AMBER does, so has to have it's own readers
etc etc. Basically it is just a mess.

This makes it a pain to port over to PMEMD. The real issue being doing it in
a way that keeps PMEMD clean since we don't want to repeat going down the
Sander route. It also needs to be done carefully such that it doesn't just
destroy the performance. So I think if we are to port stuff just saying
porting the NCSU codes is NOT the way to go. The key is to identify the
specific methods one would like and the justification for why. Then go back
to the original equations for those methods and implement them in the CPU
version of PMEMD from scratch with full documentation, test cases etc. This
should also be documented in the manual. Then it should be tested in serial
and parallel and it confirmed it doesn't hurt performance. Then it can be
ported to the GPU, again with test cases etc. Then once that is done the
method should be back ported to Sander such that sander works the same way
as PMEMD and then the sander NCSU code corresponding to that should be
deleted. This way things get done in a careful, documented and user friendly
manner that can be maintained moving forward. Suffice to say I would expect
this to be a full time job for someone for a year or so to do it properly.

So I think the first thing is to audit the NCSU code and make a clear
description of specifically which methods are wanted and why. Then if you
want we could work together on trying to implement those methods in pmemd
and pmemd.cuda. The bonus being that if we do it this way it gets
incorporated in the code in a way that ensure it will be maintained moving

All the best

|\oss Walker

|            Assistant Research Professor              |
|            San Diego Supercomputer Center            |
|            Adjunct Assistant Professor              |
|        Dept. of Chemistry and Biochemistry          |
|          University of California San Diego          |
|                    NVIDIA Fellow                    |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk  |

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Received on Sun Mar 04 2012 - 18:30:02 PST
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