3DNA Forum

Questions and answers => MD simulations => Topic started by: Pablo Ricardo Arantes on February 14, 2014, 07:45:23 am

Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Title: Runing find_pair to analyze MD trajectory
Post by: Pablo Ricardo Arantes on February 14, 2014, 07:45:23 am

Hi,

I've a question about when is necessary run find_pair for analyze my MD trajectory in PDB format (output of GROMACS).
I will explain:

1) I always run find_pair for the first frame, I've a PDB file of my first frame. After that, I run analyze with this file.inp for all my MD trajectory in PDB format. It's correct?

2) I was talking with my colleague, and he said I need to generate for every frame of my MD trajectory a new file.inp with find_pair. After that, I run for every frame with different file.inp the analyze program.

I would like to know, what's the correct way to do that??

Thanks for your attention,

Best,

Pablo 

Title: Re: Runing find_pair to analyze MD trajectory
Post by: xiangjun on February 14, 2014, 07:54:10 am

Hi Pablo,

Please use the Ruby script x3dna_ensemble which automates the analysis of MD simulation trajectories. Note that you need 3DNA v2.1 for this functionality. Search the Forum for further info.

Xiang-Jun

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.