Re: How to save a structure after minimizing for 1000 steps?

From: Chitrak Gupta (
Date: Thu Apr 23 2015 - 16:35:58 CDT

Hi Arijit,

The structure should already be minimized. However, if you want to save a
frame from a dcd file, just use this Tcl script in the Tk console window

set sel [atomselect top all]
$sel frame n (n is the frame you want to save. If it is the last frame,
just put the final frame number, note that VMD counts the frames from 0).
$sel writepdb myfile.pdb

myfile.pdb file will contain the structure in the n-th frame of the dcd.


On Thu, Apr 23, 2015 at 5:15 PM, Arijit Ghosh <>

> ‎Hi everyone,
> I want to ask how do I save the structure from the dcd file after
> minimizing for 1000 steps? I'm very new to NAMD.
> Regards,
> Arijit
> Sent from my BlackBerry 10 smartphone.

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