PMC

Conformations of pentane.

Ramachandran free energy landscapes of alanine dipeptide with standard AMBER and CHARMM-MSCALE-AMBER simulations. Both free energy proffiles are very similar. Slight differences are expected even though same force field and solvent method are used since the molecular dynamics runs were performed with different packages with their own implementations of Langevin Dynamics.

ΔG as a function of window for (A) the OH move of methanol and (B) the alanine dipeptide moving from the CHARMM22 to AMBER99SB force fields. In both cases the free energy curve is smooth, representing a gradual shift from one force field or structure to another.

The sum of squares of the off diagonal upper triangular elements of the 5×5 matrix obtained by dotting the normalized shape difference vectors against one another for the ENM and all-atom cases (see section 3.4.1 for details) as a function of the weighting between the third and second order moments. Since off-diagonal elements are expected to be minimal, the optimal weighting was determined to be 0.12 in each case, but slightly higher for the ENM than the all-atom model.

Illustration of the subroutine calling sequence of the MSCALE facility; showing the information flow of a typical energy (ENER), minimization (MINI), or normal mode analysis (DIAG) calculation. The broadcast and receive routines handle both coordinate and energy/gradient communication. Routines in blue are executed on the main processor (client) while those in yellow take place on the subsystems (servers). Thin black lines represent information being passed between subroutines where the thick black lines represent MPI calls and the sharing of information between the controlling client process and the server process, which acts only as an energy, force, or Hessian engine. The EMSCALE subroutine is called twice from CHARMM’s main energy routine, once at the beginning to send the data to the servers and again at the end to receive the energy, force, etc. terms from them. Therefore, the servers and clients are performing calculations in parallel. Further details of how MSCALE is implemented is given in the .