Re: AMBER: How to get a periodic box of modified water molecules

From: David A. Case <>
Date: Wed, 3 Jan 2007 22:04:10 -0800

On Wed, Jan 03, 2007, Li Su wrote:

> I am wondering if there is a way I can get a periodic box of water
> molecules which do not have any constraints on its bonds or angles (just
> the normal water molecule, not those models like tip3p, tip4p etc.)

It's not clear what you mean by the "noraml water molecule". Tip3p is easily
the most common water model, although spc/e is in many ways better (and just
as simple).

> Plus, if it is possible, I am also wondering is there a way I can change
> the mass of H to be bigger, so that I can use larger time steps when not
> using cosntraints.

If you wish to use a larger time step, all the more reason to use a rigid
water model (like tip3p, etc.). The easiest way to change the masses is
generally to hand-edit the prmtop file. You will probably want to increase
the masses of hydrogens in your solute as well as in the water, otherwise you
won't be able to get the time step increase you want. Note that with altered
masses, the "time" is no longer a physical time. If you are not an
experienced user, I would make a fairly strong pitch that you gain experience
with "standard" simulations before trying to use non-standard masses and water
models--in the long (and even short) run, you'll be more productive.

...good luck...dac

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Received on Sun Jan 07 2007 - 06:07:19 PST
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