From: Babban Mia (babbanmia_at_gmail.com)
Date: Fri Aug 12 2011 - 13:55:03 CDT
Hello
I looked through the entire tutorial and it has much more number of
parameters than specified in the above shell script.
Just a question : Apart from the few values that we setup above in the bash
script.Do all the values get assumed for some Default value ?
*cat << $name$i.namd < ENDIN** *
* #write your input stuff here*
* *
* *
* *
* ENDIN*
What does this above statement do ?
Like we can write about other input stuff about our simulation in the region
corresponding to "*#write your input stuff here*"
*$namdhome/charmrun +p ADD_UR_VALUES_HERE $namdhome/namd2 $name$i.namd *
What does +p signify ?
What does "*ADD_UR_VALUES_HERE*" signify in the above script statement ?
Please advise
Best
Babban
On Fri, Aug 12, 2011 at 11:37 PM, Ismail, Mohd F. <farid_at_ou.edu> wrote:
> All of the answer to your question is available on NAMD userguide.
>
> If you don't want to go through the userguide, just do a quick google
> search, for example "NAMD binaryrestart no"...
>
> HTH
> --Farid
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
> Babban Mia [babbanmia_at_gmail.com]
> *Sent:* Friday, August 12, 2011 12:06 PM
> *To:* Norman Geist
> *Cc:* Namd Mailing List
> *Subject:* Re: namd-l: Batch Mode MD simulation Script for NAMD
>
> 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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