I'm trying to understand the details of how various water models are handled in AMBER. More specifically, I'm adding support for 4 and 5 site water to OpenMM, and I need to know how to correctly interpret and load water molecules in prmtop files. I've been going through the documentation, data files, and source code, and there are a lot of things I don't understand.
First, the AmberTools manual says there are two "flexible water models", SPC/Fw and qSPC/Fw. Does that mean that all other water models are always rigid, regardless of the value of the ntc flag? If so, how do I recognize water moleces in the prmtop file that should be made rigid? Or is water actually made rigid or flexible based on the value of ntc, just like everything else?
Comparing the frcmod files for the "rigid" and "flexible" water models, there's only two obvious differences: the flexible ones include an angle term, and the force constant of the H-H "bond" is 0. Presumably those differences somehow encode the fact that water should be left flexible, but how? Do bonds with force constants of 0 not get constrained with ntc > 1? Or does the presence of the angle term somehow tell AMBER not to constrain the H-H distance, even though this is water and would otherwise be rigid? Or something else?
Then there's the frcmod files for TIP4P, TIP4P-Ew, and TIP5P. I don't understand those at all. The only bond they define for the extra sites is to the oxygen, which obviously isn't enough to define their positions. Looking through the source code, it appears that any atom whose name starts with EP or LP gets treated in a special way, but I don't understand the details. How do I determine the locations for these sites?
Thanks!
Peter
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Received on Mon Feb 13 2012 - 12:00:02 PST
