From: Hadi (dinpajooh_at_gmail.com)
Date: Tue Aug 05 2014 - 02:14:00 CDT
On Tue, Jul 29, 2014 at 9:21 PM, Kenno Vanommeslaeghe <
> On 07/29/2014 06:59 PM, Hadi wrote:
>> Below you can find the parameters of the modified TIP3P model (CGenFF:
>> Parameters for the Charmm General Force Field). This model is often used
>> in NAMD.
> (1) Small detail: the only thing this has to do with CGenFF is that it is
> the water model on which *all* the all-atom additive CHARMM force fields
> are based, the first one of which predates CGenFF by roughly 15 years. The
> confusion likely arises from the fact that the NAMD version of the CHARMM
> water stream file can currently be found on my CGenFF page. Instead, we
> probably should put it on the main CHARMM force field page alongside the
> CHARMM version.
> (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.
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