Re: Batch Mode MD simulation Script for NAMD

From: Babban Mia (babbanmia_at_gmail.com)
Date: Fri Aug 12 2011 - 12:59:45 CDT

Hello

I was just looking at the .config file which came along with the NAMD
tutorial.After running NAMD through that .NAMD script I think we get .coor
,.res . vel and .xsl files.

I was thinking that We need to just write a shell scrip which could just
convert the above created .pdb file from .coor file after the first run and
keep on feeding it through a shell to .config file .This would be done over
the loop in shell and hence the whole MD would be run.

Please suggest

Best Babban

On Fri, Aug 12, 2011 at 10:36 PM, Babban Mia <babbanmia_at_gmail.com> wrote:

> hanks 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 ?*
> *Do we not need a .config file as well which then has all the other vital
> information for this to run ?
> *
>
>
> 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 –eq 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 " ?
> *
>
> 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****
>>
>> ** **
>>
>> #Generate Input for first run (cause of the different coor
>> and vel)****
>>
>> 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****
>>
>> else****
>>
>> cat << $name$i.namd < ENDIN****
>>
>> #write your input stuff here****
>>
>> ****
>>
>> 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****
>>
>> #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****
>>
>> done****
>>
>> ** **
>>
>> exit 0****
>>
>> ** **
>>
>> ** **
>>
>> ** **
>>
>> Hope this helps…feel 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, 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:* 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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