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

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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

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University