211 related articles for article (PubMed ID: 21469158)
1. Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5.
Abraham MJ; Gready JE
J Comput Chem; 2011 Jul; 32(9):2031-40. PubMed ID: 21469158
[TBL] [Abstract][Full Text] [Related]
2. Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms.
Barash D; Yang L; Qian X; Schlick T
J Comput Chem; 2003 Jan; 24(1):77-88. PubMed ID: 12483677
[TBL] [Abstract][Full Text] [Related]
3. Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities.
Gruber CC; Pleiss J
J Comput Chem; 2011 Mar; 32(4):600-6. PubMed ID: 20812321
[TBL] [Abstract][Full Text] [Related]
4. Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations.
Sagui C; Pedersen LG; Darden TA
J Chem Phys; 2004 Jan; 120(1):73-87. PubMed ID: 15267263
[TBL] [Abstract][Full Text] [Related]
5. Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions.
Róg T; Murzyn K; Pasenkiewicz-Gierula M
Acta Biochim Pol; 2003; 50(3):789-98. PubMed ID: 14515159
[TBL] [Abstract][Full Text] [Related]
6. Force field dependence of phospholipid headgroup and acyl chain properties: comparative molecular dynamics simulations of DMPC bilayers.
Prakash P; Sankararamakrishnan R
J Comput Chem; 2010 Jan; 31(2):266-77. PubMed ID: 19475632
[TBL] [Abstract][Full Text] [Related]
7. Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation.
Wennberg CL; Murtola T; Páll S; Abraham MJ; Hess B; Lindahl E
J Chem Theory Comput; 2015 Dec; 11(12):5737-46. PubMed ID: 26587968
[TBL] [Abstract][Full Text] [Related]
8. Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals.
Schnieders MJ; Fenn TD; Pande VS
J Chem Theory Comput; 2011 Apr; 7(4):1141-56. PubMed ID: 26606362
[TBL] [Abstract][Full Text] [Related]
9. Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems.
Kikugawa G; Apostolov R; Kamiya N; Taiji M; Himeno R; Nakamura H; Yonezawa Y
J Comput Chem; 2009 Jan; 30(1):110-8. PubMed ID: 18524021
[TBL] [Abstract][Full Text] [Related]
10. Gaussian split Ewald: A fast Ewald mesh method for molecular simulation.
Shan Y; Klepeis JL; Eastwood MP; Dror RO; Shaw DE
J Chem Phys; 2005 Feb; 122(5):54101. PubMed ID: 15740304
[TBL] [Abstract][Full Text] [Related]
11. On mesh-based Ewald methods: optimal parameters for two differentiation schemes.
Stern HA; Calkins KG
J Chem Phys; 2008 Jun; 128(21):214106. PubMed ID: 18537414
[TBL] [Abstract][Full Text] [Related]
12. A GPU-Accelerated Fast Multipole Method for GROMACS: Performance and Accuracy.
Kohnke B; Kutzner C; Grubmüller H
J Chem Theory Comput; 2020 Nov; 16(11):6938-6949. PubMed ID: 33084336
[TBL] [Abstract][Full Text] [Related]
13. ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.
Marsili S; Signorini GF; Chelli R; Marchi M; Procacci P
J Comput Chem; 2010 Apr; 31(5):1106-16. PubMed ID: 19824035
[TBL] [Abstract][Full Text] [Related]
14. Effects of long-range electrostatic forces on simulated protein folding kinetics.
Robertson A; Luttmann E; Pande VS
J Comput Chem; 2008 Apr; 29(5):694-700. PubMed ID: 17849394
[TBL] [Abstract][Full Text] [Related]
15. The influence of different treatments of electrostatic interactions on the thermodynamics of folding of peptides.
Baumketner A; Shea JE
J Phys Chem B; 2005 Nov; 109(45):21322-8. PubMed ID: 16853765
[TBL] [Abstract][Full Text] [Related]
16. Multilevel summation method for electrostatic force evaluation.
Hardy DJ; Wu Z; Phillips JC; Stone JE; Skeel RD; Schulten K
J Chem Theory Comput; 2015 Feb; 11(2):766-79. PubMed ID: 25691833
[TBL] [Abstract][Full Text] [Related]
17. Analytical Hessians for Ewald and particle mesh Ewald electrostatics.
Simmonett AC; Brooks BR
J Chem Phys; 2021 Mar; 154(10):104101. PubMed ID: 33722046
[TBL] [Abstract][Full Text] [Related]
18. Accelerating molecular modeling applications with graphics processors.
Stone JE; Phillips JC; Freddolino PL; Hardy DJ; Trabuco LG; Schulten K
J Comput Chem; 2007 Dec; 28(16):2618-40. PubMed ID: 17894371
[TBL] [Abstract][Full Text] [Related]
19. jSimMacs for GROMACS: a Java application for advanced molecular dynamics simulations with remote access capability.
Roopra S; Knapp B; Omasits U; Schreiner W
J Chem Inf Model; 2009 Oct; 49(10):2412-7. PubMed ID: 19852516
[TBL] [Abstract][Full Text] [Related]
20. Performance enhancements for GROMACS nonbonded interactions on BlueGene.
Abraham MJ
J Comput Chem; 2011 Jul; 32(9):2041-6. PubMed ID: 21469156
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]