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CHARMM TIP3P model or classic TIP3 model?
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Each time when we run pdb2gmx in gromacs, if we select charmm36 FF for our system, we always have following informations:
Select the Water Model:
1: TIP3P TIP 3-point
2: TIP4P TIP 4-point
3: TIPS3P CHARMM TIP 3-point with LJ on H's (note: twice as slow in GROMACS), recommended for lipids
4: SPC simple point charge
5: SPC/E extended simple point charge
6: None
Do we really need CHARMM TIP3P model for our system, especially for membrane system? That's could be very important issue since the simulation speed will decrease dramatically if we introduce this TIP3P solvent model, comparing with traditional TIP3P model.
three-site models have three interaction sites, corresponding to the three atoms of the water molecule. Each atom gets assigned a point charge, and the oxygen atom also gets the Lennard-Jones parameters. The 3-site models are very popular for molecular dynamics simulations because of their simplicity and computational efficiency. Most models use a rigid geometry matching the known geometry of the water molecule. An exception is the SPC model, which assumes an ideal tetrahedral shape (HOH angle of 109.47°) instead of the observed angle of 104.5°.
The table below lists the parameters for some 3-site models.
| TIPS | SPC | TIP3P | SPC/E | |
|---|---|---|---|---|
| r(OH), Å | 0.9572 | 1.0 | 0.9572 | 1.0 |
| HOH, deg | 104.52 | 109.47 | 104.52 | 109.47 |
| A × 10−3, kcal Å12/mol | 580.0 | 629.4 | 582.0 | 629.4 |
| B, kcal Å6/mol | 525.0 | 625.5 | 595.0 | 625.5 |
| q(O) | −0.80 | −0.82 | −0.834 | −0.8476 |
| q(H) | +0.40 | +0.41 | +0.417 | +0.4238 |
The SPC/E model adds an average polarization correction to the potential energy function:
where μ is the dipole of the effectively polarized water molecule (2.35 D for the SPC/E model), μ0 is the dipole moment of an isolated water molecule (1.85 D from experiment), and αi is an isotropic polarizability constant, with a value of 1.608 × 10−40 F m2. Since the charges in the model are constant, this correction just results in adding 1.25 kcal/mol (5.22 kJ/mol) to the total energy. The SPC/E model results in a better density and diffusion constant than the SPC model.
The TIP3P model implemented in the CHARMM force field is a slightly modified version of the original. The difference lies in the Lennard-Jones parameters: unlike TIP3P, the CHARMM version of the model places Lennard-Jones parameters on the hydrogen atoms too, in addition to the one on oxygen. The charges are not modified.
According to Gromacs CHARMM FF paper (J. Chem. Theory Comput., 2010, 6 (2), pp 459–466
DOI: 10.1021/ct900549r), as indicated in the benchemark, no obvious differences were found between CHARMM TIP3P model and traditional TIP3P model. More extensive discussions can be found in both Gromacs and CHARMM commnunity:
http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=23727
http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=23422#Post23422
http://pubs.acs.org/doi/full/10.1021/ct900549r
http://lists.gromacs.org/pipermail/gmx-users/2010-September/053966.html
It seems that most people holde similar opinions towards this question. Actually, in one of the recent De.Shaw CELL paper (Cell (2013), 152 (3), 557–569), they also introduced normal TIP3P water model+ CHARMM36 FF for their system. In this work, they performed 100+ us long time scaled MD simulation for an extremely large membrane protein and the results were supported well by biochemical experiments.
Reference:
http://en.wikipedia.org/wiki/Water_model
CHARMM & GROMACS community
https://blog.sciencenet.cn/blog-355217-706357.html
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