TiReX: Replica-exchange molecular dynamics using Tinker

Computer Physics Communications

Volumn 180, Issue 10, 2009, Pages 2013-2019

  Penev, Evgeni S ^a   Lampoudi, Sotiria ^b   Shea, Joan Emma ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California   (United States)

Author keywords

Fortran 90 95; Molecular dynamics; MPI; Replica exchange method; Tinker molecular modeling package

Indexed keywords

CATALOGUE IDENTIFIERS; COUPLED CLUSTERS; DISTRIBUTED PROGRAM; DRIVER PROGRAM; FORTRAN 90/95; IRELAND; MESSAGE PASSING INTERFACE; MPI; OPERATING SYSTEMS; PARALLELIZATIONS; PROGRAMMING LANGUAGE; REPLICA-EXCHANGE METHOD; REPLICA-EXCHANGE MOLECULAR DYNAMICS SIMULATIONS; RUNNING TIME; SOLUTION METHODS; TEST DATA; TIME INTERVAL; TINKER MOLECULAR MODELING PACKAGE;

COMPUTER OPERATING SYSTEMS; CORROSION PREVENTION; DYNAMICS; MESSAGE PASSING; MOLECULAR DYNAMICS; MOLECULAR MODELING; SOLAR CONCENTRATORS; TEST FACILITIES;

FORTRAN (PROGRAMMING LANGUAGE);

EID: 69349104215     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2009.06.005     Document Type: Article

References (34)

1. Frenkel D., and Smith B. Understanding Molecular Simulation. Computational Science vol. 1 (2001), Academic Press, San Diego, CA
2. Hansmann U.H.E., and Okamoto Y. Numerical comparisons of three recently proposed algorithms in the protein folding problem. J. Comput. Chem. 18 (1997) 920-933
3. Sugita Y., and Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314 (1999) 141-151
4. Zhang W., Wu C., and Duan Y. Convergence of replica exchange molecular dynamics. J. Chem. Phys. 123 (2005) 154105
5. Periole X., and Mark A.E. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. J. Chem. Phys. 126 (2007) 014903
6. Sindhikara D., Meng Y., and Roitberg A.E. Exchange frequency in replica exchange molecular dynamics. J. Chem. Phys. 128 (2008) 024103
7. Nymeyer H. How efficient is replica exchange molecular dynamics? An analytic approach. J. Chem. Theory Comput. 4 (2008) 626-636
8. Case D.A., Cheatham III T.E., Darden T., Gohlke H., Luo R., Merz Jr. K.M., Onufriev A., Simmerling C., Wang B., and Woods R. The AMBER biomolecular simulation programs. J. Comput. Chem. 26 (2005) 1668-1688. http://ambermd.org/
9. Brooks B., Bruccoleri R., Olafson D., States D., Swaminathan S., and Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4 (1983) 187-217. http://www.charmm.org/
10. Lindahl E., Hess B., and van der Spoel D. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 7 (2001) 306-317. http://www.gromacs.org/
11. Plimpton S.J. Fast parallel algorithms for short-range molecular dynamics. J. Comput. Phys. 117 (1995) 1-19. http://lammps.sandia.gov
12. M. Sears, S. Plimpton, M. Rintoul, Parallel tempering Monte Carlo in LAMMPS, Report SAND2003-4113, Sandia, Nov. 2003
13. Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa C.C.E., Skeel R.D., Kalé L., and Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26 (2005) 1781-1802
14. Feig M., Karanicolas J., and Brooks III C.L. MMTSB tool set: Enhanced sampling and multiscale modeling methods for applications in structural biology. J. Mol. Graph. Model. 22 (2004) 377-395. http://mmtsb.org/
15. Eleftheriou M., Rayshubski A., Pitera J.W., Fitch B.G., Zhou R., and Germain R.S. Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L. Proceedings of the 20th International Parallel and Distributed Processing Symposium. April 25-29, 2006, Rhodes Island, Greece (2006), IEEE Computer Society Press 8 pp
16. Nymeyer H., Gnanakaran S., and García A.E. Atomic simulations of protein folding, using the replica exchange algorithm. Methods Enzymol. 383 (2004) 119-149
17. Thachuk C., Shmygelska A., and Hoos H. A replica exchange Monte Carlo algorithm for protein folding in the HP model. BMC Bioinformatics 8 (2007) 342-361
18. Bellesia G., Lampoudi S., and Shea J.-E. Computational methods in nanostructure design: Replica exchange simulations of self-assembling peptides. In: Gazit E., and Nussinov R. (Eds). Nanostructure Design: Methods and Protocols. Methods in Molecular Biology vol. 474 (2008), Humana Press, Totowa, NJ 133-151 (Ch. 9)
19. Patriksson A., and van der Spoel D. A temperature predictor for parallel tempering simulations. Phys. Chem. Chem. Phys. 10 (2008) 2073-2077
20. Abraham M.J., and Gready J.E. Ensuring mixing efficiency of replica-exchange molecular dynamics simulations. J. Chem. Theory Comput. 4 (2008) 1119-1128
21. Ren P., and Ponder J.W. Polarizable atomic multipole water model for molecular mechanics simulation. J. Phys. Chem. B 107 (2003) 5933-5947. http://dasher.wustl.edu/tinker/
22. Shen M.-Y., and Freed K. Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models. Biophys. J. 82 (2002) 1791-1808
23. Liang T., and Walsh T.R. Molecular dynamics simulations of peptide carboxylate hydration. Phys. Chem. Chem. Phys. 8 (2006) 4410-4419
24. Penev E., Ireta J., and Shea J.-E. Energetics of infinite homopolypeptide chains: A new look at commonly used force fields. J. Phys. Chem. B 112 (2008) 6872-6877
25. Paizs B., Baker J., Suhai S., and Pulay P. Geometry optimization of large biomolecules in redundant internal coordinates. J. Chem. Phys. 113 (2000) 6566-6572
26. Shen M.-Y., and Freed K. A simple method for faster nonbonded force evaluations. J. Comput. Chem. 26 (2005) 691-698
27. The Message Passing Interface (MPI) standard. http://www-unix.mcs.anl.gov/mpi/
28. Chodera J.D., Swope W.C., Pitera J.W., Seok C., and Dill K.A. Use of weighted histogram analysis method for the analysis of simulated and parallel tempering simulations. J. Chem. Theory Comput. 3 (2007) 26-41. https://simtk.org/home/ptwham
29. The running time for this example is 21.5 hours on a Intel Xeon cluster (1 Dual-Core processor per node, 2.8 GHz, 2 × 512 KB L2 Cache, 4 GB RAM) with Dolphin Interconnect, and 6 hours on an AMD Opteron cluster (2 Dual-Core processors per node, 2.6 GHz, 4 × 1 MB L2 Cache, 8 GB RAM) with Myrinet 2000 Interconnect
30. Smith P.E. The alanine dipeptide free energy surface in solution. J. Chem. Phys. 111 (1999) 5568-5579
31. Ponder J.W., and Case D.A. Force fields for protein simulations. Adv. Prot. Chem. 66 (2003) 27-85
32. Chekmarev D.S., Ishida T., and Levy R.M. Long-time conformational transitions of alanine dipeptide in aqueous solution, Continuous and discrete-state kinetic models. J. Phys. Chem. B 108 (2004) 19487-19495
33. Drozdov A.N., Grossfield A., and Pappu R.V. Role of solvent in determining conformational preferences of alanine dipeptide in water. J. Am. Chem. Soc. 126 (2004) 2574-2581
34. Chodera J.D., Swope W.C., Pitera J.W., and Dill K.A. Long-time protein folding dynamics from short-time molecular dynamics simulations. Multiscale Model. Simul. 5 (2006) 1214-1226