We want to implement NpT ensemble calculations in our parallel MD
code but are not sure how to do it. I looked at Berendsen's paper,
and at the information in McCammon and Harvey, but the equations don't
seem correct. Specifically, Berendsen's says:
__ -> ->
P=(2/3 V) ( E + 0.5 \ r . F )
k /_ ij ij
i<j
->
E is the kinetic energy , r is the vector from i to j
k ij
->
and F is the force on j from i
ij
Now, my problem is that this equation assumes there are only pair-wise
forces, but we use the CHARMm parameter set; with angles, dihedrals,
etc. These cannot be broken down into pair-wise forces, so the above
equation doesn't work for MD.
Am I correct? And if so, does anyone have a reference to a paper
that tells how to include the higher body terms?
Andrew Dalke
dalke at ks.uiuc.edu