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Re: Question about Urea parameters (Caflisch and Karplus, 1995)
lennart #25297 09/02/10 06:03 PM
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I don't think we did cite that-- for water, we focused mainly on viscosity results with P-M Ewald, which is about 1/3 the experiment value at 20 deg C, but has a different T dependence than experiment. We examined carbohydrate diffusion and viscosity as a function of [sugar] for the new carbohydrate force field.


Rick Venable
computational chemist

Re: Question about Urea parameters (Caflisch and Karplus, 1995)
rmv #25302 09/02/10 09:08 PM
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Thank you for the comments.

I think I didn't say clearly enough about the interaction energy.

The values shown in my previous post is the sum of only vdW and electrostatic energy. So, the most difference comes from electrostatic energy and I think this results from a different charge distribution in Dr. Nilsson's force field.

Is there any advantage in that asymmetric charge distribution ?

Re: Question about Urea parameters (Caflisch and Karplus, 1995)
cola #25304 09/02/10 09:41 PM
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The interaction energy has no other contributions than vdW and Coulomb, so this is sort of obvious. If you read our paper you will find the rationale behind the charge distribution - basically fitting to a published QM-based model. We made no comparisons to the Caflisch model.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Question about Urea parameters (Caflisch and Karplus, 1995)
rmv #25306 09/02/10 09:46 PM
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OK, you basically reproduce our old results then, with PME coming out slightly worse. No big surprise since TIP3P was not parametrized with PME. I think there is a TIP4P-PME model in the literature - how do your results compare with that in terms of differneces for he water model with and without PME?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Question about Urea parameters (Caflisch and Karplus, 1995)
lennart #25307 09/02/10 09:49 PM
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I should have read you paper before I asked that question.
Thank you.

Re: Question about Urea parameters (Caflisch and Karplus, 1995)
cola #25309 09/02/10 10:02 PM
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It is a good thing that you will now read the paper. Perhaps you will also read the Caflisch&Karplus paper. These forums are NOT, and certainly were never intended to be, a substitute for real learning - read the primary literature, do your homework, try things out for yourself, test your ideas.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Question about Urea parameters (Caflisch and Karplus, 1995)
lennart #25325 09/04/10 11:22 PM
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Just FYI, there's yet another urea model in CGenFF. I believe Alex put it together (but don't take my word for it). It might be interesting to test it along with the others.

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