[gmx-users] Doubts regarding Simulation box - Thanks

Kavyashree M hmkvsri at gmail.com
Fri Jan 14 06:30:53 CET 2011

Thanks Tsjerk and Mark!

After setting the box I measured the distance of the last protein
atom and the box edge it was not same all the sides. Any comments on this?

I have sent another question regarding minimization but no replys yet.
Kindly reply Sir!

Thanking you

On Fri, Jan 14, 2011 at 10:42 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> 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.
> Mark
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