VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sun Jan 22 2017 - 07:48:30 CST

>
> is it possible to minimize the recorded structures during a long
> namd simulation run

Yes. You will need to do some work to get this done though.

is it possible do this on the all recorded structures in the DCD file after
> namd termination

Yes.

with a single configuration file

Yes. You would probably need just one configuration file, but you would
need to do some shell processing around it.

e.g.

read trajectory
using a for loop in tcl write each frame (or as many frames you want) out
as a PDB file
using a shell/python script pass each individual frame to a conf file
(standard energy minimization script :: available from the tutorial here ::
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win.pdf) which
minimises its input file when done with frame delete it/or keep it -- save
output file/energy value.

The above method is just one of the ways you can do this. Another would be
to use the loop within the same conf file. But the above is what I would
like, since I have many intermediate steps.

On Mon, Jan 23, 2017 at 1:43 AM, saeed amini <aminisaeed1_at_gmail.com> 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
> 

-- 
Best,
/A