MD simulations

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Subject / Started by	Replies / Views	Last post
Analysis of PDB file:query Started by souviksur	5 Replies 11715 Views	April 19, 2012, 12:18:08 pm by xiangjun
analyzing longer DNA sequences Started by shynomat	5 Replies 8944 Views	November 21, 2012, 11:05:56 am by xiangjun
3dna.pl - A Perl Script for Parsing 3DNA Output Started by slaw	5 Replies 10148 Views	February 10, 2011, 10:29:25 pm by xiangjun
average values from MD simulations Started by ara	4 Replies 8775 Views	March 20, 2011, 10:50:35 am by xiangjun
A-Form B-Form RNA/DNA Started by drknnetz	4 Replies 16218 Views	March 23, 2017, 10:44:59 am by xiangjun
How is the helix axis calculated in 3DNA Started by wwang02	4 Replies 8756 Views	September 29, 2014, 11:33:18 pm by wwang02
Analysis of Amber .mdcrd File Started by rwmolt	3 Replies 14730 Views	June 15, 2017, 12:07:32 pm by xiangjun
How to fix the phosphate on the DNA backbone Started by tpc2005	3 Replies 10065 Views	November 20, 2016, 03:31:26 am by tpc2005
"Ruby in cygwin" Started by bciezah1	3 Replies 13690 Views	April 06, 2017, 10:59:33 am by bciezah1
the sign of minor or major groove width Started by shahabshariati	3 Replies 8107 Views	February 10, 2011, 10:06:26 pm by xiangjun
do_x3dna as a plugin for VMD and update in dnaMD Started by Rajendra Kumar	3 Replies 14918 Views	May 27, 2019, 12:16:26 pm by xiangjun
Filter frayed ends or broken H bonds Started by RAHULRAH	3 Replies 16428 Views	October 11, 2019, 08:54:11 am by xiangjun
Using find_pair Started by jdap1989	3 Replies 7873 Views	September 18, 2012, 11:33:25 pm by xiangjun
Average or Global properties from a simulation Started by metoo	2 Replies 11269 Views	March 24, 2017, 07:45:55 am by metoo
DNA screwing into protein Started by vito_genna	2 Replies 8714 Views	October 14, 2013, 08:42:15 am by vito_genna
pdb files created using v 1.5 and v 2.1 beta Started by shynomat	2 Replies 6964 Views	May 29, 2012, 09:03:44 pm by xiangjun
About output files from x3dna_md.rb Started by Pablo Ricardo Arantes	2 Replies 8762 Views	September 07, 2012, 10:07:09 pm by Pablo Ricardo Arantes
How to generate a Methylated DNA pdb file from sequence to be use in MD Started by bciezah1	2 Replies 13863 Views	June 23, 2017, 10:52:57 am by bciezah1
No matching entry in atomlist.dat Started by shynomat	2 Replies 7116 Views	May 02, 2012, 01:42:02 pm by shynomat
generate DNA pdb file for Gromacs Started by dailiang	2 Replies 23092 Views	October 27, 2021, 01:00:46 pm by dnalectronics

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.

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