Re: AMBER: high temperature, 498K, unfolding simulations

From: Andreas Svrcek-Seiler <svrci.tbi.univie.ac.at>
Date: Thu, 13 Nov 2003 18:05:46 +0100 (CET)

Hi,
> I have noticed in a recent paper (PNAS vol 100, p13287) from Daggett's and
> Fersht's groups that they have been using a 2fs time step at 498K
> (although they weren't using AMBER). I am wondering if such a long time
> step is a good idea at this temperature and am currently running
> simulations with 1fs time steps and 2fs time steps at 500K to see what
> differences there are.
I'd say that as long as it's numerically stable, it's ok. MD at 498 K
is a way to untangle a structure but not to obtain the actual behavior
of the respective molecule at that temperature (does anyone know
the boiling temperature of TIP3P water ?) - That's only my personal
opinion. Others (with more experience) might have a different opinion.

Best regards
Andreas

-- 
             
            )))))
            (((((
           ( O O )
-------oOOO--(_)--OOOo-----------------------------------------------------
              o        Wolfgang Andreas Svrcek-Seiler  
              o        (godzilla) 
                       svrci.tbi.univie.ac.at
      .oooO            Tel.:01-4277-52733 
      (   )   Oooo.    
-------\ (----(   )--------------------------------------------------------
        \_)    ) /
              (_/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Thu Nov 13 2003 - 17:53:01 PST