Hello,
I am trying to wrap my head around the parameters in Amber's tip3p.frcmod file.
With the help of this tutorial (
https://www.mpikg.mpg.de/6106699/Tutorial_ModifyingAmber_ff14SB_parameters_v07_AVV.pdf) and the frcmod file format specs (
https://ambermd.org/FileFormats.php), I believe I have worked out how most of the parameters come into play, but I am left with a couple lingering questions:
BOND
OW-HW 553.0 0.9572 TIP3P water
HW-HW 553.0 1.5136 TIP3P water
Most TIP3P descriptions provide an O-H bond length (9.572A) and an angle (104.52deg). I've deduced that the H-H bond length here (1.5136A) can be calculated from those values via law of cosines. However, I am still perplexed as to the value of 553. The frcmod spec states that this is the harmonic force constant, in units of kcal/mol/(A**2). Yet, TIP3P is a rigid model, so are these values even relevant? Where did this specific value come from? Would changing it be significant? What would happen if someone ran a simulation without using the SETTLE algorithm to keep the water rigid?
Thank you,
Austin Paul
Software Engineer
Wyss Institute
Harvard University
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Received on Thu Feb 18 2021 - 16:30:02 PST
