Theoretical Seminars: Difference between revisions
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== Next Theoretical Seminar == | == Next Theoretical Seminar == | ||
TBA. | |||
== Suggested topics == | == Suggested topics == | ||
Line 32: | Line 27: | ||
#Of the history of MD: differences between all these forcefields that we always talk about: GROMOS, CHARMM, OPLS, AMBER, GROMACS, GAFF... | #Of the history of MD: differences between all these forcefields that we always talk about: GROMOS, CHARMM, OPLS, AMBER, GROMACS, GAFF... | ||
#Molecular surfaces, NAccess | #Molecular surfaces, NAccess | ||
== Past Theoretical Seminars == | == Past Theoretical Seminars == | ||
=== Water models in computer simulation (Ying Xue, 03.09.09) === | |||
# [[media:Berendsen1981_SPC.pdf|Berendsen, HJC, Postma, JPM, van Gunsteren, WF and Hermans, J (1981) Interaction models for water in relation to protein hydration. ''In'' Intermolecular Forces; Reidel Ed.; Dordrecht, The Netherlands, 331–342]]: SPC model. | |||
# [[media:Berendsen1987_SPCE.pdf|Berendsen, HJC, Grigera, JR and Straatsma, TP (1987) The missing term in effective pair potentials. ''J. Phys. Chem.'' '''91''', 6269–6271]]: SPC/E model. | |||
# [[media:Jorgensen1983_TIP3P.pdf|Jorgensen, WL, Chandrasekhar, J, Madura, JD, Impey, RW and Klein, ML (1983) Comparison of simple potential functions for simulating liquid water. ''J. Chem. Phys.'' '''79''', 926–935]]: TIP3P model. | |||
# [[media:Mahoney2000_TIP5P.pdf|Mahoney, MW and Jorgensen, WL (2000) A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. ''J. Chem. Phys.'' '''112''', 8910–8922]]: TIP5P model. | |||
# [[media:Guillot_JMolLiq2002.pdf|Guillot, B (2002) A reappraisal of what we have learnt during three decades of computer simulations on water. ''J. Mol. Liq.'' '''101''', 219–260]]. | |||
===Generating the force field for a heteromolecule (Alpesh Malde, 21.05.09) === | ===Generating the force field for a heteromolecule (Alpesh Malde, 21.05.09) === |
Revision as of 05:05, 8 September 2009
Schedule
See the Group meeting schedule.
Next Theoretical Seminar
TBA.
Suggested topics
You are more than welcome to suggest topics for future theoretical seminars.
Name of topic | Suggestion by
- Structural Determination | Mitchell — Done
- How to define Clusters and what can we learn from it on proteins properties? | Itamar — Done
- Generating the force field for a heteromolecule | Alpesh — Done
- Gromacs 4: What's new - What's broken? Breaking the 2fs time step barrier and clever parallelisation.
- GROMOS2017 – New developments (Coming soon(ish)!)
- Error in Crystal/NMR Structures and their implications.
- Determination of secondary structure elements | David — Done
- SETTLE/RATTLE/timestep: methods for the simulation of water, implications in our simulations in a world that thinks the 2-fs timestep is because of the C–H bond vibration frequency.
- LINCS/SHAKE/dummy atoms
- What can be analyzed from simulations? An introduction to the various structural/dynamic properties that can be calculated
- NMA/PCA/ED: what are these methods? how good are they? what for?
- Sequence alignment, prediction of secondary structures, homology modelling
- Of the history of MD: differences between all these forcefields that we always talk about: GROMOS, CHARMM, OPLS, AMBER, GROMACS, GAFF...
- Molecular surfaces, NAccess
Past Theoretical Seminars
Water models in computer simulation (Ying Xue, 03.09.09)
- Berendsen, HJC, Postma, JPM, van Gunsteren, WF and Hermans, J (1981) Interaction models for water in relation to protein hydration. In Intermolecular Forces; Reidel Ed.; Dordrecht, The Netherlands, 331–342: SPC model.
- Berendsen, HJC, Grigera, JR and Straatsma, TP (1987) The missing term in effective pair potentials. J. Phys. Chem. 91, 6269–6271: SPC/E model.
- Jorgensen, WL, Chandrasekhar, J, Madura, JD, Impey, RW and Klein, ML (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935: TIP3P model.
- Mahoney, MW and Jorgensen, WL (2000) A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys. 112, 8910–8922: TIP5P model.
- Guillot, B (2002) A reappraisal of what we have learnt during three decades of computer simulations on water. J. Mol. Liq. 101, 219–260.
Generating the force field for a heteromolecule (Alpesh Malde, 21.05.09)
- Oostenbrink, C, Villa, A., Mark, AE and van Gunsteren, WF (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25, 1656–1676: this paper describes the GROMOS 53A5 and 53A6 force field.
- Lins, RD and Hünenberger, PH (2005) A new GROMOS force field for hexopyranose-based carbohydrates. J. Comput. Chem. 26, 1400–1412: this paper describes generating the force field for sugars.
- Seminario, JM (1996) Calculation of intramolecular force fields from second-derivative tensors. Int. J. Quantum Chem. S30, 1271-1277: this paper describes how to generate the force constants for bond, angle and dihedral terms from a Hessian matrix of the molecule in the equilibrium geometry using Hess2FF method.
Determination of secondary structure elements (David Poger, 23.04.09)
- PDF file of the talk here
- Complementary reading:
- Kabsch, W and Sander, C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (12), 2577-2637: article of reference for DSSP
- Frishman, D and Argos, P (1995) Knowledge-based protein secondary structure assignment. Proteins 23 (4), 566-579: article of reference for STRIDE
- Sklenar, H, Etchebest, C and Lavery, R (1989) Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 6 (1), 46-60: algorithm P-Curve
- Martin, J, Letellier, G, Marin, A, Taly, J-F, de Brevern, AG, Gibrat JF (2005) Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct. Biol. 5, 17.
Clustering methods (Itamar Kass, 30.10.08)
- PDF file of the talk here
- Complementary reading:
- Torda, AE and van Gunsrteren, WF (1994) Algorithms for clustering molecular dynamics configurations. J. Comput. Chem. 15 (12), 1331-1340
- Shao, J et al (2007) Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. J. Chem. Theory Comput. 3, 2312-2334
- Daura, X et al (1999) Peptide folding: when simulation meets experiment. Angew. Chem. Int. Ed. '38 (1/2), 236-240