[gmx-users] Regarding setting up the simulation box

[Mark Abraham]

Hi,

And choose your cell shape wisely. Biology need not be cubic ;-)

Mark

On Tue, 26 Sep 2017 02:27 Dallas Warren <dallas.warren at monash.edu> wrote:

> There is no "wall".
>
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
> https://twitter.com/dr_dbw/status/909559339366572032
>
> What is important is the distance with itself, through the PBC.  The
> complex should not interact with itself.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> <https://maps.google.com/?q=381+Royal+Parade,+Parkville+VIC+3052&entry=gmail&source=g>
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 19 September 2017 at 21:37, vijayakumar gosu
> <vijayakumargosu at gmail.com> wrote:
> > Dear all,
> >
> > i am performing molecular dynamics for large complex with ~500,000
> atoms. I
> > have considered cubic box with 1nm distance from the molecule to the wall
> > of the box. however this takes huge number of water molecules, hence i
> have
> > manually visualized and edited the box inorder to reduce the water
> > molecules. The complex is stable throughout dynamics for 25ns. however i
> am
> > bit skeptic whether this approach is correct, because not sure the
> molecule
> > is exactly at the center of the box and also i have not checked the
> > distance between the molecule and the wall of the box before md run.
> could
> > you please comment on it?
> >
> > Thanks
> > --
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