[gmx-users] Regarding setting up the simulation box

Dallas Warren dallas.warren at monash.edu
Tue Sep 26 02:27:37 CEST 2017

There is no "wall".



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
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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