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Which Water model for best thermodynamic properties?
#7251 06/23/05 04:28 PM
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Hi,

I did search the forum and did read some very useful discussion on tip3, tip4, and tip5 water models in terms of accuracy of protein-water interactions and viscosity measurements.

I was wondering which would be the best model for calculating thermodynamic properties of water like enthalpies ? These will be simulations of pure water.

Also, what would be an optimal size for a water box for such calculations ?

I thought I could post these questions here for some useful feedback from the experts before immersing myself deeper into literature.

Thanks very much for the help !

-Himanshu

Re: Which Water model for best thermodynamic properties?
hkhandel #7252 06/23/05 06:57 PM
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I am not sure what you want to do, but there is a high probability that it has already been done. The thermodynamic properties of these models have been thoroughly investigated, and also used in their parametrization. Check the original literature carefully.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Which Water model for best thermodynamic properties?
lennart #7253 06/23/05 07:12 PM
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Thanks for the reply, Lennart. Yes, I am aware that the thermodynamic properties of these systems would have been investigated thoroughly. That is exactly why we want to use water. We are trying to come up with a new method to calculate free energies, and want to test it on water. But needed to know which water model would be most accurate to minimize errors.

Thanks !

Re: Which Water model for best thermodynamic properties?
hkhandel #7254 06/24/05 05:27 PM
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"The best" is meaningless as you applying it to a very different models. Most of them reproducing heat of evaporization/free energy of water in water solvation/volume/etc fairly well but some of them lack to get self-diffusion and it possibly will affected viscosity too or dielectric constant or interfacial potential. Most of them being rigid models will have some troubles in getting spectral properties as well such far-IR spectra or some of ACF's too.

Since you use a general descriptor - thermodynamical properties rather than particular property it is hard or even impossible to answer your question.


Sergei Noskov snoskov@ucalgary.ca Dept.BioSciences University of Calgary
Re: Which Water model for best thermodynamic properties?
noskov #7255 06/24/05 06:35 PM
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My fault that I was not too specific. I am primarily interested in the total internal energy of the simulated system and secondarily in the free energy (A at constant NVT). I hope this makes things a little more clear? Thank you very much for the help.

Re: Which Water model for best thermodynamic properties?
hkhandel #7256 06/24/05 07:21 PM
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Internal energy you are talking about is U? I guess that people used Hevap (dH) as a measure rather than U itself. dH can be measured experimentally. dH= kT - dU.

TIP3P as well as others are fine in getting of this property ~9.8 kcal/mol to 10.1 kcal/mol. TIP3P is too fast with self-diffusion D ~5 vs experimentally measure 2.
Another "problem" is reported dimer interation energy in TIP3P, which is a bit more negative than conventional ab-initio estimates.

Last edited by noskov; 06/24/05 09:01 PM.

Sergei Noskov snoskov@ucalgary.ca Dept.BioSciences University of Calgary
Re: Which Water model for best thermodynamic properties?
noskov #7257 06/25/05 02:24 PM
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It would seem to me that if you are developing a method to calculate free energies of solvation, it is not important that the model is accurate with respect to reproducing experiment, but rather that the free energy of solvation of the model has been calculated to high precision using different methods. this will allow for comparison of your method with previously published works. there are some recent papers by Pande and Roux on free energies of sovlation that may be helpful.

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: Which Water model for best thermodynamic properties?
noskov #7258 07/25/05 08:05 PM
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Hi,

We have in mind a new method to calculate free energies in general. We have applied it to Argon, and it works well. We do not want to move to proteins before we work on simpler models like water. Thus, solvation is not what we are looking for. We are trying to calculate the thermodynamics properties (internal energy and free energy) of pure water only. Looks like TIP3P will be an adequate model ? For this kind of work, computational cost is not a limiting factor, but we will need the best model possible which can match experimentally measured enthalpies and free energies.

Thank you for the help,

-Himanshu


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