TIP3P model

From: Amit Paliwal (paliwal_at_jhu.edu)
Date: Wed Dec 17 2003 - 13:10:45 CST

Hi All,
I run simulation of small peptides in water and have a question
regarding the TIP3P water model in
par_all27_prot_lipids.inp and top_all27_prot_lipids.inp files. It gives
RESI TIP3 which specifies OH1, H1, H2 for water molecule and gives atom
types as OT and HT respectively. Now I am confused as original
TIP3P water model had LJ parameters for just O in water whereas the
parameter file gives separate sigma and epsilon values for oxygen and
hydrogens( i.e. for OT and HT ). Does NAMD then
calculates LJ energy by considering water as 3 atoms?? What is more
confusing is that the OT parametes match the original TIP3P united atom
paramter? Can anyone here help me clear this issue?
thanks,
Amit.

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