Hi Jason,
Thanks. TIP4P-FB has the same molecular geometry as the other TIP4Ps (with the virtual site in a different place). TIP3P-FB has a slightly different geometry from TIP3P. I'll look into putting the library files and solvent boxes together, following the existing examples. Looking forward to your visit by the way!
- Lee-Ping
On May 28, 2014, at 12:22 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Hi Lee-Ping,
>
> There will always be _somebody_ that will be interested ;). The basic
> necessary files would be a library file (perhaps also an equilibrated
> solvent box like TIP3P and TIP4P/TIP4Pew have) as well as any frcmod
> files that have new LJ parameters (I'm assuming the 3 bonds are the
> same).
>
> You're welcome to look through the existing files ($AMBERHOME/dat/leap/)
> as templates (maybe consulting the format specs on the file types at
> http://ambermd.org/formats.html). Alternatively, I'll be visiting your
> group come July and I can help you work on this then if you want.
>
> All the best,
> Jason
>
> On Wed, 2014-05-28 at 11:35 -0700, Lee-Ping Wang wrote:
>> 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.
>>
>> I've run several microseconds of protein simulations using TIP3P-FB
>> and TIP4P-FB in Gromacs and OpenMM, 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 This is currently unpublished work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 - and if so, which files I
>> should be providing. I'm not as familiar with AMBER as I am with
>> Gromacs / OpenMM.
>>
>> Thanks,
>>
>> - Lee-Ping Wang
>>
>> Link to the paper: https://www.dropbox.com/s/phwlr3jsnhe46bw/Wang_Pande.RigidWater.JPCL.2014.pdf
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Wed May 28 2014 - 12:30:03 PDT
