Dmitri G. Fedorov's homepage

News

19.1.12. The PIEDA/PCM paper is published and FMO references are updated.
13.1.12. The review of fragment-based methods is published and FMO references are updated.
11.1.12. The BG/P paper is published and FMO references are updated.
10.1.12. FMO portal has been reopened.
13.12.11. The following paper "Large-Scale MP2 Calculations on the Blue Gene Architecture using the Fragment Molecular Orbital Method" has been accepted for publication in the Journal of Chemical Theory and Computation.
18.11.11. The following paper "Energy Decomposition Analysis in Solution Based on the Fragment Molecular Orbital Method" has been accepted for publication to the Journal of Physical Chemistry A and FMO references are updated.
28.10.11. FMO portal is temporarily closed for maintenance.
18.9.11. FMO portal has been opened. The purpose of FMO portal is to make available developed tools, provide hightlights on recent development and exchange information among FMO users.
1.9.11. The following paper "Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method with effective potentials" has been accepted for publication in Theoretical Chemistry Accounts. FMO references are updated.
1.8.11. The following paper "Fragmentation Methods: A Route to Accurate Calculations on Large Systems" is accepted for publication to Chem. Rev (online text). The analytic FMO-MP2 gradient paper is published and FMO references are updated.
12.7.11. The following paper "Analytic energy gradient for second-order Moeller-Plesset perturbation theory based on the fragment molecular orbital method" was accepted for publication in J. Chem. Phys.
13.6.11. FMO references are updated.
2.5.11. FMO 4.1 code update is released in GAMESS and FMO references are updated.
12.4.11. The fully analytic energy gradient paper and the Springer book chapter are published and FMO references are updated.
10.3.11. The following paper "Fully analytic energy gradient in the fragment molecular orbital method" was accepted for publication in J. Chem. Phys. FMO references are updated.
25.1.11. The FMO/EFP and FMO/FD papers are published and FMO references are updated.
14.1.11. The following paper "Geometry Optimization of the Active Site of a Large System with the Fragment Molecular Orbital Method" was accepted for publication in the Journal of Physical Chemistry Letters.
7.12.10. The papers on influenza are published and FMO references are updated.
5.11.10. FMO references are updated.
28.10.10. The following paper "A combined effective fragment potential - fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin" was accepted for publication in J. Chem. Phys.
19.10.10. The following paper "Role of the key mutation in the selective binding of avian and human influenza hemagglutinin to sialosides revealed by quantum-mechanical calculations" was accepted for publication in the Journal of the American Chemical Society. online text
14.10.10. The following paper "Binding of Influenza A Virus Hemagglutinin to Sialoside Receptor is not Controlled by the Homotropic Allosteric Effect" was accepted for publication in the Journal of Physical Chemistry B. online text FMO references are updated.
6.9.10. A review of the FMO book is published.
6.9.10. The paper on point charges in FMO is published and FMO references are updated.
17.6.10. The following chapter "Mathematical Formulation of the Fragment Molecular Orbital method" has been accepted for publication to the Springer book "Linear-Scaling Techniques in Computational Chemistry and Physics/Vol.13". Springer info. This chapter has 169 equations on 42 pages, and is the most concise mathematical reference on FMO (final revision submitted 12.11.09).
16.6.10. FMO references updated.
28.5.10. The HOP derivative paper is published and FMO references are updated.
22.4.10. The following paper "The Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods" was accepted for publication in J. Phys. Chem. A in the special issue in honour of Prof Klaus Ruedenberg.
16.4.10. The following paper "Importance of the hybrid orbital operator derivative term for the energy gradient in the fragment molecular orbital method" was accepted for publication in Chem. Phys. Lett.
16.4.10. A disk cloning article was added.
16.4.10. The following paper "Systematic Study of the Embedding Potential Description in the Fragment Molecular Orbital method" was accepted for publication in J. Phys. Chem. A in the special issue in honour of Prof Klaus Ruedenberg.
13.4.10. The FMO1-NMR (merged) paper is published and FMO references are updated.
5.4.10. FMO references updated.
29.3.10. FMO references updated.
12.2.10. The following paper ""Fragment-molecular-orbital-method-based Ab initio NMR Chemical-shift Calculations for Large Molecular Systems" was accepted for publication in J. Chem. Theor. Comp.
7.11.09. The FMO/F paper is published as a communication in J. Chem. Phys.
10.2.10. FMO references are updated.
29.1.10. The FMO/PCM gradient paper is published and FMO references are updated.
13.1.10. The FMO-ROHF paper is published and FMO references are updated.
28.12.09. FMO references updated.
11.12.09. The paper on the photosynthetic reaction center is published and FMO references are updated.
20.11.09. The following paper "Open-Shell Formulation of the Fragment Molecular Orbital Method" was accepted for publication in J. Chem. Theor. Comp.
7.11.09. The FMO/F paper is published as a communication in J. Chem. Phys. and FMO references are updated.
13.10.09. FMO references are updated.
30.9.09. The following paper "The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method" was accepted for publication as a communication in the J. Chem. Phys.
9.9.09. FMO references are updated.
22.7.09. The FMO/AFO gradient energy paper is published and FMO references are updated.
9.7.09. The FMO/EFP energy paper is published and FMO references are updated.
29.6.09. FMO references updated.
25.6.09. The following paper, "Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method" is accepted for publication in Chem. Phys. Lett. online text
4.6.09. The RESPPC derivative paper is published and FMO references are updated.
2.6.09. The following paper, " A Combined Effective Fragment Potential - Fragment Molecular Orbital Method. I. The Energy Expression and Initial Applications" is accepted for publication in J. Chem. Phys.
22.5.09. Discount information for the FMO book is added.
21.5.09. The following paper, "Energy Gradients in Combined Fragment Molecular Orbital and Polarizable Continuum Model (FMO/PCM) Calculation", is accepted for publication in J. Comp. Chem. online text
18.5.09. The FMO book is published and FMO references are updated. The FMO publication count reaches 100.
16.5.09. FMO-TDDFT gradient paper is published and FMO references are updated.
8.5.09. FMO wiki updated.
7.5.09. FMO references updated.
27.4.09. FMO references updated.
23.4.09. The heparin paper is published and FMO references are updated.
22.4.09. Two papers were accepted to Chem. Phys. Lett.: "Excited state geometry optimizations by time-dependent density functional theory based on the fragment molecular orbital method" and "Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method".
9.4.09. FMO references updated.
30.3.09. FMO references updated.
24.3.09. FMO/AFO support was added to Facio modelling software.
23.3.09. A disk cloning article was added.
4.3.09. FMO-MD review is published and FMO references are updated.
17.2.09. The following paper, "Fragment molecular orbital study of the electronic excitations in the photosynthetic reaction center of Blastochloris viridis", is accepted for publication in J. Comp. Chem. online text
16.2.09. FMO references updated.
30.1.07. FMO 3.2 code update was released in GAMESS.
28.1.09. An announcement of the FMO book is added.
26.1.09. FMO references updated.
25.12.08. FMO references updated.
22.12.08. FMO references updated.
15.12.08. FMO references updated.
12.12.08. The following paper, "Structural and interaction analysis of helical heparin oligosaccharides with the fragment molecular orbital method", is accepted for publication in International Journal of Quantum Chemistry.
25.11.08. FMO references updated.
14.11.08. FMO/AFO paper is published and FMO references are updated.
10.11.08. FMO references updated.
24.10.08. The application of FMO-TDDFT to quinacridone crystals is published and FMO references are updated.
16.10.08. FMO-TDDFT/PCM is published and FMO references are updated.
19.9.08. FMO references updated.
10.9.08. A set of tools to generate RESP charges for Amber using GAMESS is posted.
20.8.08. Two papers on FMO for solid state applications are accepted for publication in J. Phys. Chem. A: (1) "Theoretical Analysis of the Intermolecular Interaction Effects on the Excitation Energy of Organic Pigments: Solid State Quinacridone" (Online text) and (2) "Covalent bond fragmentation suitable to describe solids in the fragment molecular orbital method". (Online text)
1.7.08. FMO-MD review is accepted for publication in Theochem: Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD), a quantum simulation tool for large molecular system. (Online text)
20.6.08. FMO references updated.
19.5.08. FMO references updated.
16.5.08. FMO references updated.
21.3.08. FMO references updated.
17.3.08. The following paper is accepted for publication in J. Comp. Chem.: Polarizable continuum model with the fragment molecular orbital based time-dependent density functional theory.(Online text)
16.3.08. A cloning article was added.
21.2.08. FMO references updated.
15.12.07. FMO 3.1 code update was released in GAMESS.
30.11.07. FMO references updated.
29.11.07. FMO references updated.
19.11.07. FMO references updated.
30.10.07. FMO support was added to Facio modelling software.
24.9.07. FMO references updated.
16.9.07. FMO2-TDDFT is published and FMO references are updated.
7.9.07. NMR paper with FMO1 is published and FMO references are updated.
21.8.07. A picture of the Xano cluster added.
16.8.07. FMO1-TDDFT is published and FMO references are updated.
15.8.07. FMO references updated.
14.8.07. FMO references updated.
10.8.07. The following paper is accepted for publication in Chem. Phys. Lett.: Ab Initio NMR Chemical-shift Calculations on Proteins Using Fragment Molecular Orbitals with Electrostatic Environment.
27.7.07. The FMO review is published and FMO references are updated.
26.7.07. The following paper is accepted for publication in J. Chem. Phys.: Time-dependent density functional theory based upon the fragment molecular orbital method. This is the two-body method (FMO2-TDDFT).
11.7.07. The following paper is accepted for publication in Chem. Phys. Lett.: Time-dependent density functional theory with the multilayer fragment molecular orbital method (Online text). This is the one-body method (FMO1-TDDFT).
3.7.06. Comment on Intel Fortran compiler 10.0 and MKL 9.1 posted.
24.5.07. The ubiquitin paper is published and FMO references are updated.
21.5.07. The paper on FKBP is published and FMO references are updated.
1.5.07. FMO review is accepted for publication as a Feature Article in J. Phys. Chem. A (Online text). There are 50 FMO publications up to date.
26.4.07. FMO3-MP2 paper is published and FMO references are updated.
6.4.07. The paper on FMO geometry optimisations is published: FMO references updated.
5.4.07. FMO 3.0 code update was released in GAMESS.
2.4.07. FMO references updated.
16.3.07. FMO references updated.
5.3.07. FMO references updated.
6.2.07. The following paper is accepted for publication in J. Phys. Chem. A: "The fragment molecular orbital method for geometry optimizations of polypeptides and proteins". Online text
27.12.06. The following paper is accepted for publication in J. Comp. Chem.: Change in a protein's electronic structure induced by an explicit solvent: an ab initio Fragment Molecular Orbital (FMO) study of ubiquitin. Online text
22.12.06. The following paper is accepted for publication in PROTEINS: Molecular recognition mechanism of FK506 binding protein: an all electron fragment molecular orbital study.Online text
21.12.06. FMO references updated.
13.12.06. The paper on improved FMO approximations is published, FMO references updated.
4.12.06. The PIEDA paper is published: FMO references updated.
1.11.06. secondary FMO references updated.
1.11.06. The following paper is accepted for publication in J. Comp. Chem.: On the accuracy of the three-body fragment molecular orbital method (FMO) applied to Moeller-Plesset perturbation theory. Online text
30.10.06. FMO references updated.
23.10.06. FMO references updated.
16.10.06. The following paper is accepted for publication in Chem. Phys. Lett.: Accurate quantum-mechanical calculations of large systems with the fragment molecular orbital method.
16.10.06. FMO references updated.
21.9.06. FMO references updated.
16.8.06. FMO references updated.
8.8.06. Three FMO book chapters are now published: FMO references and secondary FMO references updated.
8.8.06. K. Suzuki at U. of Niigata implemented GDDI on SGI Origin (so that FMO can be run with high parallel efficiency there).
4.8.06. The Xano cluster installed.
1.8.06. FMO references updated.
8.6.06. Secondary FMO references updated.
4.6.06 The following book "Modern methods for theoretical physical chemistry of biopolymers", ISBN: 0-444-52220-4, 400 pages, 2006, Elsevier with three FMO chapters can be ordered. Summary.
9.5.06 The manuscript "Pair interaction energy decomposition analysis" (PIEDA) was accepted for publication in the Special Issue "90 Years of Chemical Bonding" of the Journal of Computational Chemistry. PIEDA is the Kitaura-Morokuma analysis (EDA) combined with FMO. On-line text
9.4.06. A set of Intel 9.0 Fortran options to compile GAMESS is posted.
9.4.06. The FMO/PCM paper is out: FMO references updated.
6.4.06. FMO references updated.
8.3.06. FMO references updated.
20.2.06. Secondary FMO references created.
17.2.06. FMO references updated.
30.1.06. FMO references updated.
23.1.06. FMO references updated.
20.1.06. FMO/PCM code is officially released (FMO 2.1).
20.1.06. FMO references updated (Claisen paper is out, see 22.10.05).
10.1.06. Very serious bug was found in MKL 7.2 (Intel BLAS library).
6.1.06. The following paper is accepted for publication in J. Comp. Chem.: "The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)". See also code update in FMO 2.1.
5.1.06. Web release of our paper on the application of FMO (see 22.10.05).
29.11.05. The CBC paper is out: FMO references updated.
21.11.05. Prerelease version of GAMESS with FMO 2.1 is being finalised and may be released shortly (possibly, December 2005).
21.11.05. Our SC|05 paper (see 23.6.05) was distinguished with the best technical paper award (PDF is available).
14.11.05. FMO references in Japanese updated. The CBC paper mentioned earlier (28.9.05) is available on-line.
22.10.05. A paper "All Electron Quantum Chemical Calculation of Entire Enzyme System Confirms The Collective Catalytic Device in The Chorismate Mutase Reaction" has been accepted for publication in the Journal of Physical Chemistry B.
20.10.05. A book chapter "Theoretical development of the fragment molecular orbital (FMO) method" has been accepted for publication in the volume "Modern methods for theoretical physical chemistry of biopolymers" to be published by Elsevier. The book will have another chapter on FMO applications. This will be the first book on the FMO method in English (there is one in Japanese). Our chapter is expected to be of value to all current and potential FMO users. More information will be given when available.
19.10.05. FMO 2.1 (beta 1) has been finished.
19.10.05. FMO references updated.
4.10.05. FMO references updated: FMO3-CC paper is out.
28.9.05. The following paper has been accepted for publication in Computational Biology and Chemistry: "Ab initio fragment molecular orbital method (FMO) applied to analysis of the ligand-protein interaction in a pheromone-binding protein."
26.7.05. FMO 2.0 has been released.
8.7.05. FMO resources added.
7.7.05. FMO references updated.
7.7.05. The second prerelease version of GAMESS with FMO 2.0 was internally distributed. The public release is expected in 1 week.
30.6.05. The following paper has been accepted for publication in the Journal of Chemical Physics: "Coupled cluster theory based upon the fragment molecular orbital method".
28.6.05. Prerelease version of GAMESS with FMO 2.0 was distributed for internal testing. The public release is expected in 1-2 weeks.
23.6.05. The following paper has been accepted for publication in the proceedings of SuperComputing 2005 (reviewed by 3 referees, 75% of manuscripts rejected) "Full Electron Calculation Beyond 20,000 Atoms: Ground Electronic State of Photosynthetic Proteins".
18.5.05. FMO references updated.
13.5.05. FMO 2.0 (beta 7) has been submitted to GAMESS for the final release, expected as planned in June following some testing period.
28.3.05. FMO references updated.
24.3.05. FMO 2.0 (beta 3) code has been been handed over to GAMESS. The release is expected June 2005.
23.3.05. An article "How to compile GAMESS on IA32" has been added.
18.3.05. FMO 2.0 (beta 1) has been finished. This is the first beta before the final release. At least two more betas are expected (the release is tentatively scheduled for May 2005).
17.3.05. FMO references updated: multilayer FMO paper is out.
1.3.05. FMO data updated to include multilayer inputs.
26.2.05. Web release of the following paper "Multilayer Formulation of the Fragment Molecular Orbital Method (FMO)".
24.2.05. Cloning article was added.
23.2.05. Proof corrections were sent back to JPCA for the following paper to appear in April 2005: "Multilayer Formulation of the Fragment Molecular Orbital Method (FMO)".
8.2.05. The site has been redesigned.