### Table 1: Molecular Dynamics Simulation Performance System MDM Conventional system

2001

Cited by 1

### Table 1. SMD molecular dynamics performance for some workstation CPUs.

"... In PAGE 4: ... Because Sigma uses a distance cutoff when computing long-range electrostatic forces, and because all other force calculations are to a bounded number of near neighbors, performance is observed to decrease roughly linearly with system size (total number of atoms). A consequence of this is that by expressing performance in terms of atomic updates per second (the product of system size and time steps per second), a figure of merit can be computed for any given computation platform (see Table1 ). This can then be used to determine expected performance given the size of the protein molecule (in atoms) to be simulated.... In PAGE 34: ...Table1 . SMD molecular dynamics performance for some workstation CPUs.... ..."

### Table 3: Two-Year Comparison of Molecular Dynamics Simulation Performances System MDM this year Conventional system MDM last year

2001

Cited by 1

### Table 1. Molecular band system

1991

"... In PAGE 6: ... The molecular band system is the same as that employed by Park7 and involves the electronic states of molecular oxygen, neutral and ionized molecular nitrogen, and nitric oxide. The molecular band transitions considered and the mean time to spontaneous emission are listed in Table1 . The actual time to emission in the simulation is assumed to be exponentially distributed about this mean time.... In PAGE 6: ... One restriction in modeling radiation is that the collision routine time step must be less than the minimum radiative lifetime1. As can be seen from Table1 , some of the lifetimes are quite small. Thus, when radiation is... ..."

Cited by 1

### Table 1. Molecular band system

1991

"... In PAGE 6: ... The molecular band system is the same as that employed byPark 7 and involves the electronic states of molecular oxygen, neutral and ionized molecular nitrogen, and nitric oxide. The molecular band transitions considered and the mean time to spontaneous emission are listed in Table1 . The actual time to emission in the simulation is assumed to be exponentially distributed about this mean time.... In PAGE 6: ... One restriction in modeling radiation is that the collision routine time step must be less than the minimum radiative lifetime 1 . As can be seen from Table1 , some of the lifetimes are quite small. Thus, when radiation is... ..."

Cited by 1

### Table 1. Timings in cpu seconds and energy conservation in a.u. / ps for Car{Parrinello (CP) and Born{Oppenheimer(BO) molecular dynamics simulations of a model system for 1 ps of trajectory on an IBM RS6000 / model 390 (Power2) workstation using the CPMD package 142; see Fig. 5 for corresponding energy plots. Method Time step (a.u.) Convergence (a.u.) Conservation (a.u./ps) Time (s)

2000

"... In PAGE 14: ... But only a few years later an ab initio approach was implemented within the Hartree{Fock approximation 365. Born{Oppenheimer dynamics started to be- come popular in the early nineties with the availability of more e cient electronic structure codes in conjunction with su cient computer power to solve \interesting problems quot;, see for instance the compilation of such studies in Table1 in a recent overview article 82. Undoubtedly, the breakthrough of Hohenberg{Kohn{Sham density functional theory in the realm of chemistry { which took place around the same time { also helped a lot by greatly improving the \price / performance ratio quot; of the electronic structure part, see e.... In PAGE 31: ... Conserved energy Econs de ned in Eq. (48) from Car{Parrinello (CP) and Born{ Oppenheimer (BO) molecular dynamics simulations of a model system for various time steps and convergence criteria using the CPMD package 142; see text for further details and Table1 for the corresponding timings.... In PAGE 32: ... 5(top). The computer time needed in order to generate one picosecond of Car{Parrinello trajectory increases { to a good approximation { linearly with the increasing time step, see Table1 . The most stable Born{Oppenheimer run was performed with a time step of 10 a.... In PAGE 33: ... The toy system investigated here (see Fig. 5 and Table1 ), i.e.... ..."

Cited by 5

### Table 3. System of units for molecular dynamics simulation of a Lennard- Jones particle system. The quantity kB is Boltzmann apos;s constant, with value kB = 1:38 10?23 J/K.

"... In PAGE 13: ... Similarly other quantities of interest can be represented in reduced units. We have included Table3 from Gould and Tobochnik [58] which speci es the system of units for particles in a Lennard-Jones potential. Table 3.... In PAGE 15: ... bondsO-H b = 450:0 kcal/mol, beq = 0:957 A H-H b = 450:0 kcal/mol, beq = 1:514 A angleH-O-H = 55:0 kcal/mol, eq = 104:52 systems, the parameters , and m are set to 1. Table3 can be used to interpret the computed results in a manner which is physically meaningful for argon. An important advantage of the reduced unit system is that the same simulation could be used to study a system other than argon, substituting appropriate conversion parameters analogous to the last column of the table.... ..."

### Table 3. System of units for molecular dynamics simulation of a Lennard- Jones particle system. The quantity kB is Boltzmann apos;s constant, with value kB = 1:38 10?23 J/K.

"... In PAGE 13: ... Similarly other quantities of interest can be represented in reduced units. We have included Table3 from Gould and Tobochnik [58] which speci es the system of units for particles in a Lennard-Jones potential. Table 3.... In PAGE 15: ... bondsO-H b = 450:0 kcal/mol, beq = 0:957 A H-H b = 450:0 kcal/mol, beq = 1:514 A angleH-O-H = 55:0 kcal/mol, eq = 104:52 systems, the parameters , and m are set to 1. Table3 can be used to interpret the computed results in a manner which is physically meaningful for argon. An important advantage of the reduced unit system is that the same simulation could be used to study a system other than argon, substituting appropriate conversion parameters analogous to the last column of the table.... ..."

### Table 3. The Average Total Energies and their Components (in kcal/mol) of the Alkali Metal Complexes of 1 Obtained from Molecular Dynamics Simulationsa

"... In PAGE 6: ...Sungu Hwang et al. This is confirmed from the average Coulombic energy component given in Table3 . The Coulombic energies of Li+- 1 and Na+-1 are lower than those of Na+-1 and K+-1 by 37.... In PAGE 6: ... Therefore, it is expected that the vdW interaction is the most favorable for Li+-1, followed by Na+- 1 and then by K+-1. This is confirmed by the average vdW energy components given in Table3 . The vdW energies of Li+-1 and Na+-1 are lower than those of Na+-1 and K+-1 by 2.... In PAGE 6: ...he energy cost, i.e., the strain for achieving the optimal con- formation of the host is the largest for Li+-1. The intramolec- ular energy component Vintra, as a measure of strain imposed on 1, is listed in Table3 . The amounts of strain imposed on Li+-1 and Na+-1 are larger than those on Na+-1 and K+-1 by 10.... ..."

### TABLE 1: Parameters Used in the JDM Model of trans-2- Butene Diffusion in Zeolite MEL at 623 K, Evaluated from the Molecular Dynamics Simulations at Infinite Dilution parameter

1998