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Author Topic: Runing find_pair to analyze MD trajectory  (Read 2999 times)

Offline Pablo Ricardo Arantes

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Runing find_pair to analyze MD trajectory
« on: February 14, 2014, 07:45:23 am »

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,



Offline xiangjun

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Re: Runing find_pair to analyze MD trajectory
« Reply #1 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.


Dr. Xiang-Jun Lu [律祥俊]


Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.