AMBER Archive (2003)

Subject: Re: AMBER: monte carlo

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Fri Oct 10 2003 - 09:19:41 CDT

Hi,
> As far as I know Amber has not incorporated a program to run monte
> carlo simulations? Couls tell me if I am right or not? If I am not right
> could you please give me some hints how to do it? and if I am right
> could you please indicate me software packages widely used for this purpose?
...I hope I got the question right. MC with macromolecules is quite
complicated. If you want a 'good' move set, i.e. one that allows fast
sampling (much faster than MD) and a low rejection rate, you have to spend
a lot of thinking/programming. Moving even a 'naked' backbone locally
entails
simultaneously changing 7 torsion angles (in general), or 4 consecutive
atoms. Add to this side chains, rings and so on and you see why it's
complicated. In addition, one needs to assure detailed balance,
which complicates such a procedure even more.
I've written a joke/fake paper on the problem 3 years ago,
you could have a look at it at
http://www.tbi.univie.ac.at/~svrci/frot4new.ps.gz,
remember it was written as a joke, but the 'derivation'
and literature references are correct.
Remo Rohs wrote his (very good) thesis on this, which can
be found at
http://www.diss.fu-berlin.de/2003/3/index.html
Alas, it's in german, but judging from your email address,
this should be no problem.
Maybe he'd give you the program he wrote (based on JUMNA,
solely for nucleic acids) if you ask him.

Good lock, happy MCing
Andreas 

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              o        (godzilla) 
                       svrci_at_tbi.univie.ac.at
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