NpT ensemble calculations

Andrew Dalke dalke at uxa.cso.uiuc.edu
Thu Jan 12 19:40:51 EST 1995


  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




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