Re: [AMBER] changing water molecules in water box

From: David Case <>
Date: Thu, 2 Feb 2017 15:54:38 -0500

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.


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Received on Thu Feb 02 2017 - 13:00:04 PST
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