Re: distance filter during data analysis

From: Souvik Sinha (
Date: Wed May 09 2018 - 00:53:43 CDT

 I think you can write a tcl script to extract frames of your interest as
separate pdb files using VMD (Tk Console interface). Or you can just do the
same to write only the frame numbers (fulfilling distance criteria) in a
index file (.ndx) and parse that file (.ndx) to the 'trjconv' module of
Gromacs to get a trajectory of your selected frames.


On Wed, May 9, 2018 at 10:13 AM, Dhiraj Srivastava <>

> Hi All
> I have a trajectory file from which I want to extract out the
> frames which fulfill certain distance criteria between two atom pair. what
> is the best way to do it?
> Thank you
> Dhiraj

Souvik Sinha
Research Scholar
Bioinformatics Centre
Bose Institute
Contact: 033 25693275

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