Thank you for your response. I understand that for the pure water case. I am trying to simulate glycine in water however. If I use OPLS or AMBER, as has been done frequently on the literature, my glycine water mixing rules are different. This solute solvent interaction is my source of confusion. Sorry I wasn't more clear.
Sent from my iPhone
> On Oct 4, 2015, at 10:31 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
>> On Sun, Oct 4, 2015 at 2:32 AM, conor parks <coparks2012.gmail.com> wrote:
>>
>> Thanks for the help. Just to clarify, amber in no way changes the SPC/e or
>> tip3p paramaters during the overall force field parameters determination,
>> correct? I am just trying to rationalize in my head how it is possible to
>> simulate using OPLS/TIP3P and amber/TIP3p if the mixing rule are different
>> but the water force field parameters are the same.
>
>
> One thing I'll point out is that for both SPCE and the TIPnP water models,
> the hydrogen Lennard-Jones are zero. What this means is that the only
> Lennard-Jones terms that exist in pure water are between oxygen atoms. One
> of the nice results of this is that combining rules *do not matter*.
> Geometric and arithmetic means are identical for an atom type interacting
> with itself (sqrt(sig*sig) == (sig+sig)/2). So TIP3P and SPCE are the same
> in OPLS as they are in force fields that use the Lorentz-Berthelot
> combining rules (protein-water interactions differ, but that is to be
> expected as the force fields themselves are different, but the water-water
> interactions are still the same).
>
>
>
>> Perhaps the force field
>> themselves were determined via parameter optimization in conjunction with
>> the tip3p model and SPC/E model. Can anyone clarify if this is the case for
>> amber?
>
>
> The definitive source for this information is in the force field
> parametrization papers. But the charges are derived via RESP, so the
> solvent does not come in at all there (unlike CHARMM, which I believe
> optimizes charges for use in their modified TIP3P model). I don't *think*
> the parameters are heavily optimized inside explicit solvent (i.e., to a
> specific solvent model), but the articles are the place to find this
> information for sure.
>
> I am looking in the GAFF file, but I don't see any reference to
>> SPC/e water atoms. However, in the mod4 section the epsilon value for
>> oxygen is 0.1520, but I believe the original 1983 paper had it as 0.1521.
>> Just trying to make sure I am not missing something.
>
> The water models are in frcmod.<water model> -- so look for frcmod.spce
> (and the default TIP3P parameters are in parm10.dat -- look for OW and
> HW). I can't speak to the discrepancy between 0.1520 and 0.1521, but I can
> verify that TIP3P has epsilon=0.1520 for the oxygen in the Amber force
> fields.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sun Oct 04 2015 - 10:00:03 PDT
