From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Aug 05 2014 - 09:54:35 CDT
On 08/05/2014 03:14 AM, Hadi wrote:
> (2) It is my understanding that the parameters you copy-pasted into
> your e-mail are just "reasonable values" for in case an MD engine or
> methodology is used that does not support rigid water. They won't give
> the exact same properties as the true rigid TIP3P model. NAMD,
> however, does support rigid water; assuming the psf is generated
> correctly, all one need to do is put the following line in the NAMD input:
> rigidBonds water
> Though if you're using the CHARMM force field, it's actually
> recommended to instead use
> rigidBonds all
> because that's what the force field is parametrized for.
>
>
> I hope it is clear that unlike MC simulations, a rigid model can actually
> be slightly flexible in MD simulations.
>
> Hadi
Umm no, provided that no mistakes were made in the set-up of SHAKE
(rigidBonds in NAMD), a rigid model is really rigid in MD. Except for
insignificant numerical deviations related to the SHAKE tolerance. More
info here: http://www.ks.uiuc.edu/Research/namd/1.5/ug/node64.html
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