Re: Python based tool for analysis of DCD trajectories

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Mar 09 2018 - 12:28:42 CST

Hi Harish,

Recompiling VMD for python support is also a valid option, and is what I use so that I can use VMD's atomselection syntax, which I learned first and know better. You can also compile VMD as a python module (see https://github.com/Eigenstate/vmd-python). LOOS is another option for python-based trajectory analysis (http://loos.sourceforge.net/). What I like about python enabled VMD is that I don't need to spend time coding up wrappers for external libraries that I might want to use. Basically every library under the sun these days has a python interface. The same cannot be said for Tcl.

-Josh

On 03/09/2018 07:46 AM, Brian Radak wrote:
You are definitely correct in eschewing ASCII formats like XYZ for large-scale analysis.

VMD is generally the recommended tool for trajectory analysis, substituting a Tcl interface for Python. I understand that a lot of new users find this a bit annoying since Python seems to be the tool of choice these days (I certainly had the same opinion when I started out), but spending time to learn Tcl can be advantageous and satisfying for a number of reasons (not exhaustive):

1) it can naturally interface with the VMD back-end (vectorized and GPU accelerated measurements, natural language selection, etc)
2) it has very good support for Tk and thus can be fairly easily converted to a GUI plugin for yourself and/or posterity
3) Tcl is generally more portable than Python, especially if you want to work with data remotely on supercomputers

Python still might be a good tool for your purposes, but VMD and Tcl may also be an excellent choice.

Cheers,
BKR

On Fri, Mar 9, 2018 at 1:52 AM, Haohao Fu <fhh2626_at_gmail.com<mailto:fhh2626_at_gmail.com>> wrote:
you can use MDtraj(http://mdtraj.org/1.9.0/EDwy%2BLcyjRvv2RAhMYqesZR%2B7f5GwU5OQYHyl4%3D&reserved=0>), MDanalysis(https://www.mdanalysis.org/ts9ezQol48HDRBTgfJB3beEYXaxe8nE8ZOvfqMOVA%3D&reserved=0>) or prody(http://prody.csb.pitt.edu/1YpHkR9IgqBZfYnHU3DMZl0dZcV2U%2Fs7NzYaA83Q%3D&reserved=0>) to do such things.

Haohao

2018-03-09 13:46 GMT+08:00 Harish Srinivasan <harishlglk1992_at_gmail.com<mailto:harishlglk1992_at_gmail.com>>:
I am using NAMD to simulate various systems like bilayer, micelles, eutectic solvents etc. Most of my analysis is using the trajectories of the system (i.e. x,y,z coordinates of the atom). So far I have been using catdcd to convert my dcd trajectory files to xyz format and then use it for further analysis.

Is there any particular tool (preferably python based) that can in principle allow me to get the (x,y,z) coordinates from DCD file based on, different selections of residues/segments/atom_number etc?

Thank you
Harish

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