[gmx-developers] One more correction for Amber FF

Igor Leontyev ileontyev at ucdavis.edu
Sun Apr 17 04:46:17 CEST 2011

The original parameters of TIP3P model published in JCP 79, 926 (1983) are: 
sigma=3.15066 A, eps=0.15207 kcal
which is different from all mentioned above values. In fact, the slight 
variation of TIP3P parameters across different force fields is known. As I 
remember, in CHARMM it is also different. But I don't think that such little 
variations can result in noticeable problems. There are much more 
significant concerns regarding other parameters.

    For example, all non-polarizable force field use integer formal charges 
for ions and ionized residues (e.g. +1 for Na+) such that interaction 
between them q*q/r is treated as in vacuum. But it is well known that in the 
condensed phase, relevant for biological applications, all particles are 
surrounded by electrons of neighbors. The dielectric property of this 
electronic jelly is measurable and is given by optic dielectric constant of 
the material, with typical value Eps(opt)~2.  Thus, actual interactions 
between ions obviously should be screened by the dielectric factor of 1/Eps 
= 1/2 in respect to that in vacuum. But according to the conventional 
non-polarizable concept all simulations disregard this fact, i.e. 
overestimate interactions between ions as well as between ions and water . . 

    Anyhow, it seems to be reasonable to have in gromacs parameters inherent 
for a given force field in order to be able reproduce exactly the energies 
calculated by native code.

Leontyev Igor

> So in other words, Amber isn't actually using TIP3P, then.  So the 
> question
> is, does one use AMBER, or does one use TIP3P.  This is actually a pretty
> hard call.  And actually, sounds like something the AMBER people should be
> changing.  I don't know a good solution.
> Another question is, what's the practical difference?  I might actually 
> take
> a look at this. . .
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821

>>>>>> Current vdW parameters of Amber TIP3P water (OW atom) are slightly
>>>>>> different from those in Sorin's Amber port: "3.15076e-01 
>>>>>> 6.35968e-01".
>>>>>> Later are in excellent agreement with the original amber TIP3P
>>>>>> parameters:
>>>>>> R*=1.7683 A and Eps= 0.1520 Kcal/mol.
>>>>> Sorry but can you be more specific? Is there a new parameterization of
>>>>> TIP3P in Amber? For which force fields?
>>>> OW parameters in gromacs port of amber (all versions 94-03) differ from
>>>> the
>>>> parameters in the original Amber program. Suggested correction in
>>>> amberXX.ff/ffnonbonded.itp:
>>>> ;OW           8      16.00    0.0000  A   3.15061e-01  6.36386e-01
>>>> OW           8      16.00    0.0000  A   3.15076e-01  6.35968e-01
>>> Have you tried to email Eric Sorin (cc'ed in this email) to ask about
>>> this?
>>> I suspect he could explain better.
>> As I understand, the slight difference appeared due to rounding. TIP3P
>> parameters in port of  Eric Sorin are taken from the paper Mahoney &
>> Jorgensen (2000). J. Chem. Phys. 112, 8910-8922, where the parameters 
>> are:
>> sigma=3.15061 A, eps=0.1521 kcal/mol.
>> While the parameters in original Amber parm99.dat file are
>> R*=1.7683 A (i.e. sigma=3.15075) eps=0.1520 kcal/mol.
>> Thus, to achieve an exact correspondence of forces and energies obtained
>> with Gromacs and Amber codes we need to use the original amber 
>> parameters,
>> as suggested above.

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