MD simulations

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Subject / Started by	Replies / Views	Last post
Update of do_x3dna package Started by rkumar	1 Replies 256142 Views	February 22, 2025, 11:23:27 pm by xiangjun
Looking for a way to speed up do_x3dna process. Started by Karn4132	1 Replies 155094 Views	February 15, 2026, 11:15:42 pm by xiangjun
Clarification on how DNA radius is computed from 3DNA/DSSR Started by Mamta	1 Replies 97457 Views	February 03, 2026, 09:25:43 am by xiangjun
generate DNA pdb file for Gromacs Started by dailiang	7 Replies 413188 Views	September 29, 2025, 07:45:22 am by rkumar
Base pair number not staying constant in simulations Started by piia600	2 Replies 240342 Views	May 30, 2025, 01:09:55 pm by rkumar
Do I need gromacs to use dnaMD for simulations? Started by piia600	3 Replies 258127 Views	May 20, 2025, 03:20:40 am by piia600
overwritten output files Started by Mamta	3 Replies 237105 Views	January 13, 2025, 10:47:57 am by xiangjun
Gromacs missing ' P ' atom Started by mouxuank	1 Replies 213828 Views	May 27, 2024, 06:41:08 pm by xiangjun
DNA step parameters Started by dnalectronics	0 Replies 274248 Views	October 27, 2021, 09:18:45 am by dnalectronics
Superimpose representative cluster of a RNA strand after simulation Started by Sruthi0412	1 Replies 295159 Views	November 10, 2020, 06:55:08 pm by xiangjun
Unnatural base pair helical parameters Started by sarkagaku	5 Replies 308951 Views	October 03, 2020, 07:50:35 am by sarkagaku
Failed Downloading MD Ruby Scripts of 3DNA Started by Moi Zhang	7 Replies 311345 Views	September 16, 2020, 10:38:01 am by xiangjun
Filter frayed ends or broken H bonds Started by RAHULRAH	3 Replies 229234 Views	October 11, 2019, 08:54:11 am by xiangjun
do_x3dna as a plugin for VMD and update in dnaMD Started by Rajendra Kumar	3 Replies 220190 Views	May 27, 2019, 12:16:26 pm by xiangjun
Analysis of helical parameter of DNA with unnatural Started by priyabrata das	8 Replies 245880 Views	March 01, 2019, 08:16:55 am by xiangjun
Analysis of major groove and minor groove Started by xroxzero	1 Replies 192909 Views	November 20, 2017, 12:00:07 pm by xiangjun
about "curavture" and "tangent" in dnaMD Started by xroxzero	1 Replies 234469 Views	November 08, 2017, 12:02:40 pm by Rajendra Kumar
local helical axis vector for strongly bent DNA Started by adihau	10 Replies 277156 Views	November 01, 2017, 06:41:45 am by Rajendra Kumar
How to analyze helical parameters of DNA with unnatural bases Started by shengxiehuang	1 Replies 185584 Views	September 18, 2017, 10:38:50 pm by xiangjun
How to generate a Methylated DNA pdb file from sequence to be use in MD Started by bciezah1	2 Replies 204499 Views	June 23, 2017, 10:52:57 am by bciezah1

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