[gmx-developers] Contributing new water models

[Lee-Ping Wang]

Hi Michael,

Thanks for helping me with this. :)

The comparisons for the temperature dependent data with TIP4P-Ew and TIP4P/2005 is given in the SI ( http://pubs.acs.org/doi/suppl/10.1021/jz500737m/suppl_file/jz500737m_si_001.pdf ); there are more properties here as well.

Here are the stronger trends that I could see:

1) TIP4P-FB, TIP4P-Ew and TIP4P/2005 are more accurate than TIP3P-FB for the density vs. temperature.
2) TIP3P-FB and TIP4P-FB are more accurate than TIP4P-Ew and TIP4P/2005 for the dielectric constant vs. temperature.
3) TIP3P-FB, TIP4P-FB and TIP4P/2005 are more accurate than TIP4P-Ew for the diffusion constant and shear viscosity vs. temperature.

Thanks,

- Lee-Ping

----- Original Message -----
From: "Michael R. Shirts (mrs5pt)" <mrs5pt at eservices.virginia.edu>
To: gmx-developers at gromacs.org
Sent: Wednesday, May 28, 2014 7:10:53 PM
Subject: Re: [gmx-developers] Contributing new water models

I'm happy to manage putting this in for 5.1 if people want to add it. 

Just wondering, what does the temperature dependent data look like compared to TIP4P-Ew or TIP4P/2005? Those are better water models than the original TIP3P or TIP4P, but I only saw the single point data for those water models, vs. the temperature dependent properties in Fig. 3. 

Best, 
~~~~~~~~~~~~ 
Michael Shirts 
Assistant Professor 
Department of Chemical Engineering 
University of Virginia 
michael.shirts at virginia.edu 
(434)-243-1821 

From: Lee-Ping Wang < leeping at stanford.edu > 
Reply-To: " gmx-developers at gromacs.org " < gmx-developers at gromacs.org > 
Date: Wednesday, May 28, 2014 at 1:11 PM 
To: " gmx-developers at gromacs.org " < gmx-developers at gromacs.org > 
Subject: [gmx-developers] Contributing new water models 

Dear developers, 

I'd like to contribute the following water models that were published in our recent article, "Building force fields - a systematic, automatic and reproducible approach." The models, called TIP3P-FB and TIP4P-FB, are reparameterized versions of the TIP3P and TIP4P models; they have identical functional forms and computational cost, just different parameters. They are highly accurate for reproducing the thermodynamic, kinetic and structural properties of liquid water across a wide temperature and pressure range. The .itp files are attached in their final form. 

I've run several microseconds of protein simulations using TIP3P-FB and TIP4P-FB, and they are highly compatible with the AMBER protein force fields (more specifically, amber99sb, amber99sb-ildn and amber99sb-nmr). In fact, replacing TIP3P with TIP3P-FB tends to improve the stability of the "fast folding" proteins in D.E. Shaw's paper, and it also improves the prediction of NMR J-couplings and chemical shifts. This is currently unpublished work but I'm working on a manuscript. 

Please let me know if there's interest. I think it could make sense to bundle this with the main Gromacs distribution, because the water models come with atom types that need to go into "ffnonbonded.itp" for the various implemented force fields. 

Thanks, 

- Lee-Ping Wang 

Link to the paper: https://www.dropbox.com/s/phwlr3jsnhe46bw/Wang_Pande.RigidWater.JPCL.2014.pdf 


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