On Fri, Jul 16, 2021, Dave Cerutti wrote:
>>From ${AMBERHOME}/test/tip5p/prmtop:
>
>*%FLAG MASS*
>*%FORMAT(5E16.8)*
>* 1.60000000E+01 1.00800000E+00 1.00800000E+00 3.00000000E+00
>3.00000000E+00*
>
>That's for TIP5P water atoms *O H1 H2 EP1 EP2*. I cannot understand
>this. Not at all. At what point were virtual sites ever assigned any
>mass--they would then be atoms, and the diffusion coefficient would be way
>off (not to mention the system density).
Back in prehistoric times, extra points were handled as "regular" atoms, but
that hasn't been true for several decades now. You should, however, run a
sanity check: change the masses in the prtmop file, and see if that has any
effect on a short simulation.
....dac
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Received on Fri Jul 16 2021 - 07:30:02 PDT
