AW: Batch Mode MD simulation Script for NAMD

From: Norman Geist (
Date: Fri Aug 12 2011 - 07:02:29 CDT

yes, the same would be possible with a simple bash script, I thought it
would better to not restart the simulation, and just do the pdb saving on
the fly. But if you want to do it, it could work like this:
#The loop (do prod_runs times each_steps fs runs)
            echo structure $psffile > $name$i.namd
            echo binaryrestart no >> $name$i.namd
            #Generate Input for first run (cause of the different coor and
            if [ $i -eq 1 ]; then
                        echo velocities myvelocities.vel >> $name$i.namd
                        echo coordinates mycoordinates.pdb >> $name$i.namd
            #Generate Input for rest of runs
                        cat << $name$i.namd < ENDIN
                        #write your input stuff here
                        #Here come the tricky counting things
                        #For the Input
                        echo coordinates myprod$temp.coor >> $name$i.namd
                        echo velocities myprod$temp.vel >> $name$i.namd
                        #For the Output
                        echo outputname $name >> $name$i.namd
                        #The runtime
                        echo numsteps $each_steps >> $name$i.namd
            #The input should be ready so call namd with the generated
            $namdhome/charmrun +p ADD_UR_VALUES_HERE $namdhome/namd2
            #copy the final coor of every run to pdb because it's not binary
and so already in pdb format
            cp $name$i.coor $name$i.pdb
exit 0
Hope this helps.feel free to ask
Norman Geist.
Von: [] Im Auftrag
von Babban Mia
Gesendet: Freitag, 12. August 2011 12:47
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: namd-l: Batch Mode MD simulation Script for NAMD
Hello Everyone

Thanks Norman for the information.

I am not sure about what you are suggesting. Normally what I did in CHARMM
was heating and equilibration my system for 1ns and 1ns each and I would
then have a .res file at the end of the equilibration which I would then use
to start my actual PRODUCTION run of 1ps each for a total of say 10,000
steps giving me 10ns of production run and I would say .res file at each 1ps
and start over from that new .res file for another 1ps and so on.

This was all being managed through a BASH SHELL SCRIPT.
Looking at the config file of NAMD ,I though something similar could be done
in NAMD as well.
Is it?

All I want is some easy way to run my MD for a good 100ns and save PDBs for
each 1ps.

Please advise further

Best regards

On Fri, Aug 12, 2011 at 11:17 AM, Norman Geist
<> wrote:
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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