Thank you Dr. Dac
On Thu, Feb 2, 2017 at 3:54 PM, David Case <david.case.rutgers.edu> wrote:
> On Thu, Feb 02, 2017, Lara rajam wrote:
>
> > I am trying to do an explicit water based simulation of a DNA 10
> basepair.
> > When I put a water box of size and type solvateoct 8 it has more number
> of
> > water molecules for eg. 35000. Is it possible for me to add
> approximately
> > 10000 water molecules inside the box using leap to reduce the
> computational
> > cost and will it affect the dynamics of the system anyway by doing it so
> .
> > Since the density will be maintained the same in MD, any comments will be
> > useful for better understanding
>
> 10000 water molecules won't do a very good job of solvating a 10-basepair
> DNA. You already have only 8 Ang. between the DNA and the edge of your
> box,
> and this is quite small. We usually use buffers in the range of 12-15 Ang.
> So my recommendation is to use more waters, not fewer.
>
> ...dac
>
>
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Received on Thu Feb 02 2017 - 13:30:03 PST
