User contributions for Romano
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17 April 2012
- 13:3113:31, 17 April 2012 diff hist 1,345 bytes m DsDNA persistence length →Persistence length of a double-stranded DNA
- 13:1813:18, 17 April 2012 diff hist 12,858 bytes Documentation →Configuration file
- 13:1813:18, 17 April 2012 diff hist 12,856 bytes Documentation →Configuration and topology files
- 13:1013:10, 17 April 2012 diff hist 2,656 bytes m Features of the previous version →Supported features
- 12:0012:00, 17 April 2012 diff hist 12,156 bytes Documentation →Configuration and topology files
- 11:2311:23, 17 April 2012 diff hist 2,654 bytes m Features of the previous version →Supported features
- 11:2211:22, 17 April 2012 diff hist 11,871 bytes m Documentation →Generation of input files
- 11:2211:22, 17 April 2012 diff hist 11,860 bytes m Documentation →Generation of input files
- 11:2111:21, 17 April 2012 diff hist 11,864 bytes m Documentation →Generation of input files
- 11:2111:21, 17 April 2012 diff hist 11,863 bytes Documentation →Generation of input files
- 11:1511:15, 17 April 2012 diff hist 11,490 bytes m Documentation →Generation of input files
- 11:1411:14, 17 April 2012 diff hist 11,474 bytes Documentation →Generation of input files
- 11:1311:13, 17 April 2012 diff hist 2,643 bytes Features of the previous version →Supported features
- 11:1211:12, 17 April 2012 diff hist 10,926 bytes Documentation →Configuration and topology files
- 11:0611:06, 17 April 2012 diff hist 10,783 bytes Documentation No edit summary
- 10:5710:57, 17 April 2012 diff hist 10,745 bytes m Documentation →pdb format
- 10:5610:56, 17 April 2012 diff hist 10,746 bytes m Documentation →xyz format
- 10:5510:55, 17 April 2012 diff hist 10,793 bytes m Documentation →Visualisation of structures
- 10:5310:53, 17 April 2012 diff hist 2,773 bytes m Features of the previous version →Supported features
- 10:5310:53, 17 April 2012 diff hist 10,792 bytes m Documentation →pdb format
- 10:5210:52, 17 April 2012 diff hist 2,699 bytes m Features of the previous version →Supported features
- 10:5010:50, 17 April 2012 diff hist 10,792 bytes m Documentation →pdb format
- 09:5909:59, 17 April 2012 diff hist 2,653 bytes m Features of the previous version →Supported features
- 09:5709:57, 17 April 2012 diff hist 10,764 bytes Documentation →xyz format
- 09:5609:56, 17 April 2012 diff hist 10,764 bytes m Documentation →xyz format
- 09:5309:53, 17 April 2012 diff hist 10,764 bytes Documentation →Visualisation of structures
- 01:4301:43, 17 April 2012 diff hist 10,762 bytes Documentation No edit summary
16 April 2012
- 17:5917:59, 16 April 2012 diff hist 1,959 bytes Download and Installation →Installation
- 17:5717:57, 16 April 2012 diff hist 1,710 bytes Download and Installation No edit summary
- 17:5617:56, 16 April 2012 diff hist 2,658 bytes Features of the previous version →Supported features
- 17:5517:55, 16 April 2012 diff hist 2,658 bytes Features of the previous version →Supported features
- 17:5517:55, 16 April 2012 diff hist 2,657 bytes Features of the previous version →Unsupported features
- 17:5517:55, 16 April 2012 diff hist 2,657 bytes Features of the previous version →Unsupported features
- 17:4917:49, 16 April 2012 diff hist 2,263 bytes Features of the previous version →Supported features
- 17:4817:48, 16 April 2012 diff hist 2,264 bytes Features of the previous version →Supported features
- 17:4817:48, 16 April 2012 diff hist 2,263 bytes Features of the previous version No edit summary
- 17:3417:34, 16 April 2012 diff hist 1,771 bytes Features of the previous version →Supported features
- 17:2217:22, 16 April 2012 diff hist 1,164 bytes Features of the previous version No edit summary
- 17:1517:15, 16 April 2012 diff hist 349 bytes Features of the previous version No edit summary
- 17:1517:15, 16 April 2012 diff hist 348 bytes Features of the previous version No edit summary
- 17:1417:14, 16 April 2012 diff hist 346 bytes Features of the previous version New page: Since oxDNA is still in its early stages of development, we release the code as-is with all the features enabled but we only give support to some of them. In particular, we provid [[Exampl...
- 17:1017:10, 16 April 2012 diff hist 1,710 bytes Main Page →References
- 17:0817:08, 16 April 2012 diff hist 1,699 bytes Download and Installation →Download
- 17:0617:06, 16 April 2012 diff hist 1,741 bytes Main Page →oxDNA
- 17:0617:06, 16 April 2012 diff hist 1,673 bytes Download and Installation No edit summary
- 17:0617:06, 16 April 2012 diff hist 1,673 bytes Download and Installation No edit summary
- 17:0517:05, 16 April 2012 diff hist 1,629 bytes Download and Installation No edit summary
- 16:5716:57, 16 April 2012 diff hist 6,798 bytes Pseudoknot formation No edit summary
- 16:4616:46, 16 April 2012 diff hist 1,218 bytes Download and Installation →Download
- 16:4516:45, 16 April 2012 diff hist 1,168 bytes Download and Installation →Operative system
- 16:4516:45, 16 April 2012 diff hist 1,168 bytes Download and Installation →Compiler
- 16:4216:42, 16 April 2012 diff hist 1,031 bytes Download and Installation →Operative system
- 16:4216:42, 16 April 2012 diff hist 1,030 bytes Download and Installation →Requirements
- 16:4116:41, 16 April 2012 diff hist 6,776 bytes Pseudoknot formation →Option 3
- 16:4016:40, 16 April 2012 diff hist 6,775 bytes Pseudoknot formation No edit summary
- 16:3716:37, 16 April 2012 diff hist 683 bytes Download and Installation →Requirements
- 16:3616:36, 16 April 2012 diff hist 600 bytes Download and Installation New page: ==Requirements== oxDNA compilation has been thoroughly tested with gcc >= 4.1.x and icpc >= 10. oxDNA does not require any external library. If you ==Download== The source package can be...
- 16:3416:34, 16 April 2012 diff hist 6,751 bytes Pseudoknot formation No edit summary
- 16:2816:28, 16 April 2012 diff hist 6,723 bytes Pseudoknot formation New page: One of the features of the model implemented in oxDNA is that it has a three-dimensional structure, so that it automatically incorporates topological effects (see Flavio's paper). In this ...
- 16:2516:25, 16 April 2012 diff hist 90 bytes Category:Examples No edit summary
- 16:2016:20, 16 April 2012 diff hist 88 bytes Category:Examples No edit summary
- 13:3913:39, 16 April 2012 diff hist 981 bytes m Main Page No edit summary
- 13:3913:39, 16 April 2012 diff hist 982 bytes Main Page →oxDNA
- 13:3813:38, 16 April 2012 diff hist 983 bytes Main Page →Acknowledgments
- 13:3713:37, 16 April 2012 diff hist 929 bytes Publications No edit summary
- 13:3613:36, 16 April 2012 diff hist 722 bytes Publications No edit summary
- 13:3613:36, 16 April 2012 diff hist 710 bytes Publications No edit summary
- 13:3413:34, 16 April 2012 diff hist 694 bytes Publications No edit summary
- 13:3313:33, 16 April 2012 diff hist 482 bytes Publications New page: T.E. Ouldridge, A.A. Louis and J.P.K. Doye, J. Chem. Phys, 134, 085101 (2011) [http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grai...
- 13:3013:30, 16 April 2012 diff hist 988 bytes Main Page →oxDNA
15 April 2012
- 11:5911:59, 15 April 2012 diff hist empty File:Image.png uploaded a new version of "Image:Image.png" current
13 April 2012
- 21:5921:59, 13 April 2012 diff hist 7,498 bytes Documentation →Simulation options
- 21:5621:56, 13 April 2012 diff hist 7,430 bytes m Documentation →Simulation options
- 20:0620:06, 13 April 2012 diff hist 7,429 bytes Documentation →Output files
- 20:0520:05, 13 April 2012 diff hist 7,583 bytes Documentation →Output files
- 17:4517:45, 13 April 2012 diff hist 5,089 bytes m Hairpin formation →Results
- 17:4517:45, 13 April 2012 diff hist 5,099 bytes m Hairpin formation →Introduction
- 17:4417:44, 13 April 2012 diff hist 5,097 bytes m Hairpin formation No edit summary
- 17:4117:41, 13 April 2012 diff hist 4,207 bytes Hairpin formation No edit summary
- 17:3917:39, 13 April 2012 diff hist 4,192 bytes Hairpin formation →Introduction
- 17:3817:38, 13 April 2012 diff hist 4,178 bytes Hairpin formation →Introduction
- 17:3717:37, 13 April 2012 diff hist empty File:Histo MD.png No edit summary
- 17:3617:36, 13 April 2012 diff hist 4,181 bytes m Hairpin formation No edit summary
- 17:3217:32, 13 April 2012 diff hist 967 bytes Main Page →oxDNA
- 17:2517:25, 13 April 2012 diff hist 67 bytes Category:Examples New page: Here we put examples on how to use the code to study simple systems
- 17:2317:23, 13 April 2012 diff hist 40 bytes DsDNA persistence length No edit summary
- 17:2317:23, 13 April 2012 diff hist 18 bytes DsDNA persistence length New page: = Petr's example =
- 17:2117:21, 13 April 2012 diff hist 2,981 bytes Hairpin formation No edit summary
- 17:2117:21, 13 April 2012 diff hist 31 bytes Examples Examples moved to Hairpin formation current
- 17:2117:21, 13 April 2012 diff hist 2,959 bytes m Hairpin formation Examples moved to Hairpin formation
- 17:0717:07, 13 April 2012 diff hist 2,959 bytes Hairpin formation New page: = Hairpin formation = == Introduction == In this example, you will simulate a single strand of length 18 and sequence <tt>GCGTTGCTTCTCCAACGC</tt> at 334 K (~61 C) in three different ways:...
- 17:0617:06, 13 April 2012 diff hist 7,373 bytes Documentation No edit summary
- 17:0417:04, 13 April 2012 diff hist 7,409 bytes Documentation →Compilation options
- 16:5716:57, 13 April 2012 diff hist 7,419 bytes Documentation →Molecular dynamics simulations options
- 16:5616:56, 13 April 2012 diff hist 7,423 bytes Documentation →Input/output
- 16:5616:56, 13 April 2012 diff hist 7,423 bytes Documentation →Input/output
- 16:5116:51, 13 April 2012 diff hist 7,463 bytes Documentation →Simulation options
- 16:4816:48, 13 April 2012 diff hist 7,478 bytes Documentation →Simulation options
- 16:4816:48, 13 April 2012 diff hist 7,508 bytes Documentation →Simulation options
- 16:4716:47, 13 April 2012 diff hist 7,514 bytes Documentation →Simulation options