Messages

1

MD simulations / Re: generate DNA pdb file for Gromacs

« on: September 29, 2025, 07:45:22 am »

Hi,

Another option could be the Nucleic Acid Builder (NAB) (available in AmberTools) to model the 3D structure of DNA for MD simulations (https://ambermd.org/tutorials/basic/tutorial1/section2.php). I have used this one to model the DNA and performed the MD simulations.

Thanks,
Rajendra

2

MD simulations / Re: Base pair number not staying constant in simulations

« on: May 30, 2025, 01:09:55 pm »

Hi,

Apologies for the late reply. Please use  -ref option to keep the base-pairs constant. However, any parameters calculated for broken base-pairs will be of extreme values. If base-pairs are broken at the terminals, then those could be ignored during analysis by dnaMD.

Thanks,
Rajendra

3

MD simulations / Re: Do I need gromacs to use dnaMD for simulations?

« on: May 19, 2025, 12:31:02 am »

Do I need GROMACS version of dnaMD to analyze simulations or can I use the Python module of dnaMD without GROMACS for simulations?

No, dnaMD is a python package purely written in python. However, it requires output from do_x3dna,  which is now available for direct download and does not require GROMACS installation. You can use both do_x3dna and dnaMD without requiring GROMACS installation.

Thanks,

4

MD simulations / Update of do_x3dna package

« on: February 22, 2025, 11:12:53 pm »

Dear All,

I have updated the do_x3dna package for GROMACS-2025. I have built binary executable of do_x3dna that can be downloaded and used without any compilation. Most importantly, this binary package can be used with files generated by any version of GROMACS.

Thanks,
Dr. Rajendra Kumar
Associate Professor
NIPER, Mohali, India