deleramentum.net

Random Little Things

TTM2, TTM3 and TTM4 water models. Key-Value parser in FORTRAN (likely 90 or maybe 95). A script to list possible permutations of the like atoms in simple molecule(s). A script for AMBER to DL POLY conversion. Perl script for numerical Hessian calculation using DL POLY. P, D and G triply periodic minimal surfaces: P.eps. Trefoil knot made of a DNA: 1240x1370. A slab of TTM3-F water simulated using path-integral MD: 2048x2048. An illustration of the SFG technique (wave-lengths are not to scale): 1600x900.

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Random Little Things | deleramentum.net Reviews

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TTM2, TTM3 and TTM4 water models. Key-Value parser in FORTRAN (likely 90 or maybe 95). A script to list possible permutations of the like atoms in simple molecule(s). A script for AMBER to DL POLY conversion. Perl script for numerical Hessian calculation using DL POLY. P, D and G triply periodic minimal surfaces: P.eps. Trefoil knot made of a DNA: 1240x1370. A slab of TTM3-F water simulated using path-integral MD: 2048x2048. An illustration of the SFG technique (wave-lengths are not to scale): 1600x900.

<META> KEYWORDS

1 little codes

2 nose hoover chains thermostat/barostat

3 pimd/replica exchange

4 molecular graphics

5 deps

6 geps

7 c volodymyr babin

8 coupons

9 reviews

10 scam

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Random Little Things | deleramentum.net Reviews

https://deleramentum.net

TTM2, TTM3 and TTM4 water models. Key-Value parser in FORTRAN (likely 90 or maybe 95). A script to list possible permutations of the like atoms in simple molecule(s). A script for AMBER to DL POLY conversion. Perl script for numerical Hessian calculation using DL POLY. P, D and G triply periodic minimal surfaces: P.eps. Trefoil knot made of a DNA: 1240x1370. A slab of TTM3-F water simulated using path-integral MD: 2048x2048. An illustration of the SFG technique (wave-lengths are not to scale): 1600x900.

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deleramentum.net

1

PIMD/Replica-Exchange

http://www.deleramentum.net/codes/repimd/index.html

A simple C code to run path integral molecular dynamics (PIMD) for water clusters. Several trajectories can be ran in parallel at different temperatures taking advantage of the replica-exchange method. PIMD propagator is from the following papers:. J Chem. Phys. 99, 2796 (1993); DOI: 10.1063/1.465188. Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals". Mark E. Tuckerman, Bruce J. Berne, Glenn J. Martyna, and Michael L. Klein.

2

Atom permutations

http://www.deleramentum.net/codes/atom-permutations/index.html

A little script that prints out possible permutations of the like atoms in simple molecule(s). The molecule(s) here is something like [H2O]3 or [H2O]2[Na]2. For [H2O]2 (water dimer), for example, the output is as follows:. Download the script here. Or run it via CGI:.

3

TTM2.1-F, TTM3-F and TTM4-F water models

http://www.deleramentum.net/codes/ttm/index.html

TTM21-F, TTM3-F and TTM4-F potentials. C implementation of the following four water potentails:. J Chem. Phys. 131, 024501 (2009); DOI: 10.1063/1.3167790. Competing quantum effects in the dynamics of a flexible water model". Scott Habershon, Thomas E. Markland, and David E. Manolopoulos. J Phys. Chem. A, 2006, 110 (11), pp 4100-4106; DOI: 10.1021/jp056477k. The Flexible, Polarizable, Thole-Type Interaction Potential for Water (TTM2-F) Revisited". C J Burnham and S. S. Xantheas.

4

Nose-Hoover (chains) thermostat

http://www.deleramentum.net/codes/nhc/index.html

A C implementation of a propagator for the Nose-Hoover chains thermostat. The thermostat itself is described in the following papers:. Phys Rev. A 31, p.1695-1697 (1985); DOI: 10.1103/PhysRevA.31.1695. Canonical dynamics: Equilibrium phase-space distributions". William G. Hoover. J Chem. Phys. 81, p.511 (1984); DOI: 10.1063/1.447334. A unified formulation of the constant temperature molecular dynamics methods". J Chem. Phys. 97, p.2635 (1992); DOI: 10.1063/1.463940. The algorithms are from:.

5

Key-Value parser in FORTRAN

http://www.deleramentum.net/codes/kv/index.html

Key-Value parser in FORTRAN. Parser for key-value pairs that can be grouped into named sections; the sections can be nested inside other sections. An example of valid input is as follows:. Comment version = 15 forces algorithm = 1 some params = (1.0, 3.0) ewald cut = 10.0 end ewald end forces files input = 'in' output = 'out' end files end root.

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deleramentum.net

Random Little Things

TTM2, TTM3 and TTM4 water models. Key-Value parser in FORTRAN (likely 90 or maybe 95). A script to list possible permutations of the like atoms in simple molecule(s). A script for AMBER to DL POLY conversion. Perl script for numerical Hessian calculation using DL POLY. P, D and G triply periodic minimal surfaces: P.eps. Trefoil knot made of a DNA: 1240x1370. A slab of TTM3-F water simulated using path-integral MD: 2048x2048. An illustration of the SFG technique (wave-lengths are not to scale): 1600x900.

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