AW: Batch Mode MD simulation Script for NAMD

From: Norman Geist (
Date: Fri Aug 12 2011 - 00:47:19 CDT

you can just simulate your system as usual, and get the structure states out
of the dcd trajectory for the frames you want afterwards. You can also
directly save the trajectory every 1ps if you will not need the whole
trajectory. Im sure you then can capture out the frames and save to pdb with
a vmd tcl script, that's pretty easy I guess. You can do it manually while
logging the tcl commands in vmd to see which functions it calls, then write
a little script and finish. It sounds really expensive to me, too restart
the simulation so often only so save a pdb file.
Another possibility is to use the restart.coor files, because they already
in pdb format, if don't saved binary. You could save the restarts every 1ps
and then use the tcl_forces interface to rename the file, so it won't get
overwritten by the next one, I think this is the better solution.
If that's not what your searching for, sorry.
Good luck
Norman Geist.
Von: [] Im Auftrag
von Babban Mia
Gesendet: Freitag, 12. August 2011 01:56
Betreff: namd-l: Batch Mode MD simulation Script for NAMD
Hello Everyone

I am setting up a en explicit solvent MD simulation for 100ns and I want to
save my structure at every 1ps thus giving me about 100000 structures [PDB
files] of my protein.

I will be very grateful if someone could give me/share the batch mode[shell]
with a corresponding config file for a periodic boundary explicit MD
simulation .I am sure lot of people would have used NAMD in a batch mode and
it will be a good starting point to make a batch mode script for my

Much like CHARMM,I guess I would have to first store the .res file for every
1 ps of MD simulation which could then be converted to a PDB file.

Thanks again!

Best regards

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