Re: minimizing each structure of a DCD file

From: Giacomo Fiorin (
Date: Sun Jan 22 2017 - 11:28:05 CST

Yes, just loop over the trajectory frames using Tcl syntax (the user's
guide has the related documentation and some examples of this) and execute
a "minimize" command on each.


On Sun, Jan 22, 2017 at 8:21 AM, saeed amini <> wrote:

> Hi Everyone
> Hereby I would like to inform me that is it possible to minimize the
> recorded structures during a long namd simulation run? If no, is it
> possible do this on the all recorded structures in the DCD file after namd
> termination with a single configuration file?
> Best Regards

Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
Lab page:
*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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