I'm trying to run some very basic tests with a TIP4P waterbox using AMBER
format inputs in NAMD. I thought I'd also take the opportunity to compare
energies between the two programs.
A question and a comment:
1) NAMD ignores H-H bonds and instead depends on H-O-H angles for rigid
water. This is opposite the convention in AMBER and parm7 files generated
by tleap. Is there a straightforward way for tleap to generate terms?
2) My first move was to use the regression test files from AmberTools18
under /test/tip4p. There appear to be some oddities regarding the prmtop
therein. For one, the masses of the extra points are set to 3. Also, and
perhaps this is naive since it's been a long time since I dealt with this
format, but the ATOM_TYPE_INDEX section lists the types as "1 2 2 2" for
each molecule, which seems to imply that the extra points and hydrogens
have the same type.
Cheers,
Brian
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Received on Tue Jul 31 2018 - 07:30:03 PDT
