Re: Water Box Shape Changing during NVT Simulation!

From: Axel Kohlmeyer (
Date: Tue Mar 09 2010 - 03:38:09 CST


On Tue, Mar 9, 2010 at 1:03 AM, Aditya Ranganathan <> wrote:
> Thanks to all for the suggestions.
> However my question still remains and I`m sorry that I`m sounding so naive.
> Since I`ve been recalculating periodic cell values at each step and not
> keeping it the same as what it was in the first step, I was wondering if

i don't quite understand what you mean by this. you said initially, that you
did an NVT ensemble simulation. that means that in the simulation the
cell shape and size does not change. what do your mean by "step"
and "recalculate" in this context?

> this is the reason for the change of shape as I have increased the periodic
> cell values and thus allowing the system to sample the additional space and

if you increase the cell size for a dense periodic system, you will
add vacuum. this is a rather unrealistic model. specifically, if your
initial conditions are assembled from "pieces" (i.e. protein, bilayer,

> thus the change of shape. Also, will this actually have any adverse effect
> on the way the protein actually is behaving and thus the accuracy of the
> whole simulation?
> As I said, the peptides are still well inside the solvent and not peeping
> out.

from what you describe, you have one or multiple droplets and not a
dense system. this has severe consequences, since the water vaccuum
interface will induce a surface dipole potential due to the orientational
preference of water molecules in the interface. this will make the peptides
see a very different environment from a regular bulk system.

> When I turn on the periodic cell images option in VMD, do all the periodic
> cells have to be close to each other without space in between?  Please help


> me out with the same. I`ll post a screenshot with all the periodic cells
> displayed on VMD.

please do so. a picture says much more than many words in this case.

> Thanks
> Aditya
> When I switch on all the periodic cell images
> On Tue, Mar 9, 2010 at 2:35 AM, Jeffrey J. Potoff
> <> wrote:
>> Ronald Salesky wrote:
>>> Hi Aditya,
>>>>> My question also is whether the volume can still remain the same even
>>>>> with the shape of the water box changing to cylindrical? Does an NVT
>>>>> simulation place a restriction on the shape or just the total volume of the
>>>>> water box. If its just the volume, cant the water molecules just arrange and
>>>>> rearrange themselves without the volume changing but just the shape?<<
>>> My understanding is the PBC (periodic boundary condition) you have placed
>>> on your system sets a periodic cell with the x,y,z boundaries you have
>>> specified, which means the system is modeled as if it is really a periodic
>>> array of the same protein/solvent system like in a crystal. Since the
>>> solvent/protein system wants to converge to its minimum energy, the solvent
>>> shape within the cell will change. If you were to just model a single cube
>>> of water with no solute molecule it would seek its minimum energy state
>>> which would be spherical. I am learning NAMD/VMD as you are, so those more
>>> experienced may disagree with some of these points.
>> Just a point of clarification.  In a canonical (NVT) MD simulation, one is
>> minimizing the free energy of the system, not the energy.
>> --
>> ======================================================================
>> Jeffrey J. Potoff               
>> Associate Professor                       Wayne State University
>> Department of Chemical Engineering and Materials Science
>> 5050 Anthony Wayne Dr                     Phone:(313)577-9357
>> Detroit, MI 48202                         Fax:  (313)578-5815
>> ======================================================================

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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