[gmx-users] Doubts regarding Simulation box - Thanks

Mark Abraham mark.abraham at anu.edu.au
Fri Jan 14 06:12:25 CET 2011

On 01/14/11, Kavyashree M  <hmkvsri at gmail.com> wrote:
> Thank you Tsjerk for your suggestions!

Please leave old email context in so that people can find out what you are talking about. Only to you is your email so important that you might remember all the details :-)

> So according to this my minimal box size should be 
> 0.6nm in order to avoid PBS effects and due to the 
> water effects i have to set it 1nm or higher.
> So this rule is irrespective of the box type we choose
> isnt it?

1) You need a minimum amount of water between solutes to have a reasonably physical model.
2) You wish to minimize the cost of that water by the choice of box shape and size.


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