Re: membrane equilibration

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Mar 03 2011 - 18:10:06 CST

Were you using multiple-time-stepping in CHARMM? I suspect not, and
that you are in NAMD. If this is the case, you could have some
mildly pathological interactions that are not updated as often
and lead to strong velocities that result in RATTLE failures. Some
solutions are to either determine the specific atom (via it's index) and
resolve whatever may be causing the instability, or you could attempt
longer minimization/equilibration runs in hopes the unstable interaction
resolves itself. If this is indeed your situation, you'll be more
efficient if you re-run the crashing simulation, but outputting the
frames and energies every step, and then analyzing that trajectory for
the source of your RATTLE failure.

HOWEVER, all the above is just a best guess based on your mention of a
RATTLE failure. Axel is right that it's difficult to diagnose the problem
without seeing the actual output in your query. It's often useful to
cut and paste 20 or so lines around the error message, so others can see
exactly the output. With that kind of data the namd-list can be
much more helpful.

Best,
Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 217-244-1733
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
jeremy adler <jeremyeadler_at_gmail.com> writes:
> Date: Thu, 3 Mar 2011 18:03:18 -0500
> From: jeremy adler <jeremyeadler_at_gmail.com>
> To: Axel Kohlmeyer <akohlmey_at_gmail.com>
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: membrane equilibration
> 
> Hi Dr Kohlmeyer,
> 
> It seems as though the energies never come down and I get "ERROR: Constraint
> failure in RATTLE algorithm" when the program exits the minimization
> portion. Ive tried using both fixed atom as well as harmonic restraints with
> the same basic result. I had seen somewhere in the mailing list that
> periodic boundary conditions might be too small so i made them bigger only
> to have the water collapse into the membrane. Im not exactly clear why the
> energies are so he given they werent nearly as high when i was using charmm
> and it equilibrated fine then (i am using the preequilbrated membrane from a
> charmm run i conducted). I would like to use namd because i have access to a
> bluegene computer and namd functions much better on bluegene than charmm.
> 
> 
> thanks for your help,
> 
> Jeremy
> 
> On Thu, Mar 3, 2011 at 2:43 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> 
> > On Thu, Mar 3, 2011 at 2:02 PM, jeremy adler <jeremyeadler_at_gmail.com>
> > wrote:
> > > Hi
> > >
> > > I was wondering if anyone has a membrane equilbration protocol that
> > works. I
> > > tried adapting the one in the tutorial with a membrane previousely
> > > equilibrated in charmm to no avail
> >
> > jeremy,
> >
> > before stating that something doesn't work, you should explain
> > how it fails for you and why you think that this is not adequate.
> >
> > in molecular simulations, there are so many little things that
> > can matter, it is rare that there is a one-size-fits-all solution.
> >
> > cheers,
> >    axel.
> >
> > >
> > > thanks
> > >
> > > Jeremy
> > >
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com  http://goo.gl/1wk0
> >
> > Institute for Computational Molecular Science
> > Temple University, Philadelphia PA, USA.
> >

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