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JCC
2002
85views more  JCC 2002»
11 years 5 months ago
Efficiency of the multicanonical simulation method as applied to peptides of increasing size: The heptapeptide deltorphin
: The advantage of the multicanonical (MUCA) simulation method of Berg and coworkers over the conventional Metropolis method is in its ability to move a system effectively across e...
Fatih Yaar, Handan Arkin, Tarik Çelik, Bern...
JCC
2002
78views more  JCC 2002»
11 years 5 months ago
Gravitational smoothing as a global optimization strategy
: An optimization scheme for atomic cluster structures, based on exaggerating the importance of the gravitational force, is introduced. Results are presented for calculations on Le...
T. W. Whitfield, John E. Straub
JCC
2002
61views more  JCC 2002»
11 years 5 months ago
A fast pairwise evaluation of molecular surface area
: A fast and general analytical approach was developed for the calculation of the approximate van der Waals and solvent-accessible surface areas. The method is based on three basic...
Vladislav Vasilyev, Enrico O. Purisima
JCC
2002
74views more  JCC 2002»
11 years 5 months ago
Determination of the effective dielectric constant from the accurate solution of the Poisson equation
: Constant dielectric (CD) and distance-dependent dielectric (DDD) functions are the most popular and widespread in the Molecular Mechanics simulations of large molecular systems. ...
Vladislav Vasilyev
JCC
2002
81views more  JCC 2002»
11 years 5 months ago
Multiple grid methods for classical molecular dynamics
: Presented in the context of classical molecular mechanics and dynamics are multilevel summation methods for the fast calculation of energies/forces for pairwise interactions, whi...
Robert D. Skeel, Ismail Tezcan, David J. Hardy
JCC
2002
38views more  JCC 2002»
11 years 5 months ago
Four-component relativistic Kohn-Sham theory
: A four-component relativistic implementation of Kohn
Trond Saue, Trygve Helgaker
JCC
2002
51views more  JCC 2002»
11 years 5 months ago
PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods
Matthew P. Repasky, Jayaraman Chandrasekhar, Willi...
JCC
2002
80views more  JCC 2002»
11 years 5 months ago
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations
: A protocol is described for the treatment of molecular polarization in force field calculations. The resulting model is consistent in that both inter- and intramolecular polariza...
Pengyu Ren, Jay W. Ponder
JCC
2002
52views more  JCC 2002»
11 years 5 months ago
Predicted solution structure of zymogen human coagulation FVII
Lalith E. Perera, Thomas A. Darden, Lee G. Pederse...
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