Dear All,
The total charge value of the molecular fragments in the Amber force
field libraries takes 'most of the time' an integer value. This is the
case for the terminal and central fragments of the amino-acids. This
is also true for the central fragments of the nucleotides. However,
this is not correct for the terminal fragments of the nucleotides,
where the sum of the total charges of the 2 terminal fragments has
that integer value.
I wonder if there is an importance of having such an integer value for
a molecular fragment in the electrostatic interaction computation of a
protein/polynucleotide for instance, when running MD simulation in
condensed phase using the Particle mesh Ewald algorithm/a periodic box.
I wonder also if there was not not 'something' like that in Amber 5 or
6... If so, is it still true today with the last versions of the
sander/pmemd program?
Thank you,
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 13 2022 - 00:00:02 PDT
