AW: Batch Mode MD simulation Script for NAMD

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Aug 15 2011 - 00:29:43 CDT

Hi again,
 
What does .NAMD file contain ,looklike and do here ? .Can you show in an
example of how it should look like for the current script we have ?

well the *.namd file, or you can call it however you like is the
configuration file to start your namd simulation. You should better consult
the manual for the various possible parameters. In this file you set for
example your structure and coordinates, your box dimensions. You can set
constant temperature or pressure settings. You specify how many steps the
simulation should run and how long a step will be, usual 1 femtosecond. You
can just view the examples from namd homepage or somewhere else to see what
such a config file looks like.
 
Heres a link :
http://www.psc.edu/general/software/packages/namd/examples/index.php
What does binaryrestart no signify ?
While you can save such files for coordinates and velocities in simple text
file, and read it with a simple editor, you can also save the file binary to
save hard disk space. In your case, it would make sense to save the files
not binary because the restart.coor files are already pdb and you can use
them directly without any conversion.
 
 What kind of inputs would be required here which would then need to go to
.NAMD file ?
 
Write your namd configuration parameters here and it will get written to a
config file which is then used for the runs.
 
What does +p mean here ?
 
It says how many processors will get used if you have a multicore machine or
a cluster.
 
What is "ADD_UR_VALUES_HERE " ?
 
Just a spaceholder for your parameters if you have a cluster for example,
you would needfor example an additional nodelist file. Itís just some
possible configuration to the parallel startup.
 
Mit freundlichen GrŁŖen
 
Norman Geist.
 
Von: Babban Mia [mailto:babbanmia_at_gmail.com]
Gesendet: Freitag, 12. August 2011 18:17
An: Norman Geist
Betreff: Re: namd-l: Batch Mode MD simulation Script for NAMD
 
Thanks Everyone!

Thanks a lot Norman for the Script. There are certain things that I could
not quite understand.I will embed my doubts within your script.Please help
me with the doubts.
I am very new to NAMD so will basic questions as well
What does .NAMD file contain ,looklike and do here ? .Can you show in an
example of how it should look like for the current script we have ?

On Fri, Aug 12, 2011 at 5:32 PM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
Hi,
 
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:
 
!#/bin/bash
 
#Options
prod_runs=1000
each_steps=1000
name=myproduction
psffile=mypsffile.psf
namdhome=/your/path/to_namd_dir/
 
 
#The loop (do prod_runs times each_steps fs runs)
for((i=1;i<=prod_runs;i++))
do
            echo structure $psffile > $name$i.namd
            echo binaryrestart no >> $name$i.namd
    What does binaryrestart no signify ?
 
            #Generate Input for first run (cause of the different coor and
vel)
            if [ $i Ėeq 1 ]; then
                        echo velocities myvelocities.vel >> $name$i.namd
                        echo coordinates mycoordinates.pdb >> $name$i.namd
            #Generate Input for rest of runs
            else
                        cat << $name$i.namd < ENDIN
                        #write your input stuff here
                        
      What kind of inputs would be required here which would then need to go
to .NAMD file ?
                        ENDIN
                        
                        #Here come the tricky counting things
                        #For the Input
                        temp=$[$i-1]
                        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
            fi
            
            #The input should be ready so call namd with the generated
infile
            $namdhome/charmrun +p ADD_UR_VALUES_HERE $namdhome/namd2
$name$i.namd
         What does +p mean here ?
       What is "ADD_UR_VALUES_HERE " ?
            #copy the final coor of every run to pdb because itís not binary
and so already in pdb format
            cp $name$i.coor $name$i.pdb
done
 
exit 0
 
 
 
Hope this helpsÖfeel free to ask
Norman Geist.
 
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] 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
Babban

On Fri, Aug 12, 2011 at 11:17 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
Hi,
 
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, thatís 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 donít saved binary. You could save the restarts every 1ps
and then use the tcl_forces interface to rename the file, so it wonít get
overwritten by the next one, I think this is the better solution.
 
If thatís not what your searching for, sorry.
 
Good luck
 
Norman Geist.
 
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Babban Mia
Gesendet: Freitag, 12. August 2011 01:56
An: namd-l_at_ks.uiuc.edu
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
simulation.

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
Babban
 
 

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