Re: Minimization in GB-SA-E-Spikes, LINMIN

From: Andreas Svrcek-Seiler <svrci_at_tbi.univie.ac.at>
Date: Tue 16 Jul 2002 18:00:55 +0200 (CEST)

Hi,
> During minimization,
> I keep seeing energy spikes at regular
> intervals (ex 100 steps in some cases) after
> few 1000 steps. My starting configuration has
> no bumps and the energy is close to zero.
> I also have the LINMIN FAILURE message during
> minimization. I am aware of the web-page in amber
> home which discusses LINMIN issues. My question is
> how to handle the energy spikes and LINMIN failures.
...I *believe* the SA contribution to the total energy
is not everywhere differentiable, therefore possibly confusing
the minimization routine.
I'd try to do the minimization without 'gbsa'
and calculate the non-polar solvation part afterwards,
I bet it won't make much difference.

Best regards
Andreas 

-- 
             
            )))))
            (((((
           ( O O )
-------oOOO--(_)--OOOo-----------------------------------------------------
              o        Wolfgang Andreas Svrcek-Seiler  
              o        (godzilla) 
                       svrci_at_tbi.univie.ac.at
      .oooO            Tel.:01-4277-52733 
      (   )   Oooo.    
-------\ (----(   )--------------------------------------------------------
        \_)    ) /
              (_/
Received on Tue Jul 16 2002 - 09:00:55 PDT
Custom Search