From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Sep 26 2005 - 22:27:04 CDT
Unless rigid bonds are turned on (useful for a 2 fs time step), the
water molecules should be flexible. The topology and parameter files
should detail the specifics of these bonds and angle.
(note that although tip3p also defines an H-H bond, it is not needed
for NAMD).
On Sep 26, 2005, at 4:52 PM, Leonardo Sepulveda Durán wrote:
> Hello
>
> As I understand, default dynamics in namd uses a rigid TIP3P water
> model. I have read from old papers that this is a convention to save
> computer time, so in principle it could be posible to allow bond and
> angle degrees of freedom in tip3p. If this is right, How can a do a
> Simulation with flexible tip3p? what is needed? I would like to its
> effect in my system.
>
> Thanks
>
> Leonardo
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