Re: [Towhee-users] VOLNPT output: an error message?

[Marcus M. <me...@gm...>]

On Fri, Oct 3, 2014 at 4:22 AM, Aric Newton <agn...@en...>
wrote:

I am using towhee for a one box MC-NPT simulation of two montmorillonite
> layers with an interlayer space containing the counter ions and water
> molecules.  Each montmorillonite layer is treated as an individual molecule
> and moves as a unit via the *pmtracm* move probability.  I have
> previously equilibrated the system at high temperature in the NVT ensemble
> without any errors, but the output that I am getting now that I have
> switched to the NPT ensemble leaves me a bit uncertain.  In the
> *towhee_output* file, there are about 10,000 lines that read as below.
>
> * VOLNPT: move attemped in box that has a periodic bonded molecule*
> * Molecule type:      -31414*
> * Chain number:           1*
> * Box:           2*
> ...
>
> The *.pdb snapshots are being output during the simulation, but the rest
> of the output appears to be non-standard/ non-sensical- there is only one
> box in the simulation and the negative number as a molecule type seems odd.
>
>
Indeed the error messages do mean there is a problem.  When you perform a
volume move in Towhee it scales the center of mass position of all the
molecules (in a manner appropriate for the volume change) and then keeps
all of the intramolecular distances the same.  This is not possible when
the "molecule" spans the periodic images with its bonding pattern.

You would need a completely different move that scaled the intramolecular
distances for the volume change.  That would then lead to problems with any
molecule that has a rigid bond length (as the attempt to change that bond
length would result in an infinite energy) and also would be fairly
inefficient as the intramolecular distances are quite sensitive.


> The *volnpt.f* file description from the towhee code manual notes that
> “you cannot use this move with a molecule that is bonded through the
> periodic boundary condition (like a zeolite).”  I suspect that the bonds in
> the montmorillonite molecules are across the periodic boundary and trigger
> the VOLNPT output message. However, this same note is listed for the
> *volnvt.f* file and there are no warnings generated.  Are these
> simulation results corrupt?  Is there a way to salvage this simulation or
> work around this problem?  The forcefield for the interactions is CLAYFF.
> So, the bonds, angles, torsions, and improper  in the montmorillonite
> layers are zero energy.  I had to define these terms so that each
> montmorillonite layer can be a molecule that can move/ translate during the
> simulation.  Is there an alternate way to conduct this simulation and avoid
> the VOLNPT violation?
>

Only if every atom in the montmorillonite was a separate molecule.
However, be aware you are then changing the density of your montmorillonite
and it is quite likely that is not what you are intending to sample.

I'm not sure if you were intending to sample the layer separation distance,
but in that case you would need a new implementation of the volume move
that only scale the volume in one of the dimensions instead of uniformly.

Marcus

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