Re: membrane equilibration

From: jeremy adler (jeremyeadler_at_gmail.com)
Date: Thu Mar 03 2011 - 17:03:18 CST

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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