Dear all,
I wish to do some qm/mm simulation with Gaussian/Amber interface, so I look through the AMBER manual and some relavent mailing lists. But stil I got some questions.
FIrst one, the fundamental of QM/MM calculation, so far as what I understand, is to replace classical force field (eg. gaff2, etc) with quantum mechanical calculation. So for Gaussian/AMBER simulation, Gaussian will calculate the energy and force for the QM part, which is all that Gaussian do in simulation. Sander or pmemd will take care of the evolution of coordinates and velocities of the entire system, no matter the QM part or MM part, using certain algorithm, eg., leap-frog, verlet, etc. Do I make some mistakes, or are there any details that I missed?
Nest, for parallel calculation, I got confused. Under the &gau namelist, the Amber manual indeed mentioned "num_threads". So for example, if I assign 12 cpu to sander.MPI, i.e., command "mpirun -np 12 sander.MPI xxx", and set num_threads=6, then for qm part, Gaussian will use 72 cpu, or merely 6 cpu? And the number of cpu requested is the sum of sander.MPI and Gaussian, or Gaussian just takes a portion of cpu from what I assign to sander?
Any help would be appreciated.
Best regards,
Xinghe Zhang
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Received on Sun Oct 23 2022 - 21:30:02 PDT
