AW: Batch Mode MD simulation Script for NAMD

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Aug 15 2011 - 00:34:15 CDT

binaryoutput no

Mit freundlichen Grüßen

Norman Geist.

-----Ursprüngliche Nachricht-----
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Babban Mia
Gesendet: Samstag, 13. August 2011 14:37
An: Ismail, Mohd F.
Cc: Namd Mailing List
Betreff: Re: namd-l: Batch Mode MD simulation Script for NAMD

Hello

As was suggested by Norman, I built a similar shell script and it is working
fine but I think Norman assumed that output.coor files generated at the end
of one NAMD run are not the binary,
Infact they are the binary files and doing the step

*"cp $name$i.coor $name$i.pdb " *becomes redundant and more so because of
the binary nature of .coor file , the further coordinates can not be
specified for the script like *
**"echo coordinates myprod$temp.coor >> $name$i.namd" *because .coor here is
binary and thus namd does not recongnize it as a pdb file and does not load
in the coordinates for the next run.

Is there a way we can switch .coor from binary to normal?
I looked at the NAMD tutorial as well and it does say that the only non
binary files generated at the end of one script are :

   1. output_eq.xsc
   2. output_eq.restart.xsc
   3. output_eq.restart.xsc.

Please advise,if only the .coor files (in binary form) could be used to load
the coordinates for future runs,I would not have any problems or may be
there is a way to convert .coor from binary into pdb at the end of each run
with the help of simple command line.*

*Best
Babban*
*
On Sat, Aug 13, 2011 at 1:10 AM, Ismail, Mohd F. <farid_at_ou.edu> wrote:

> The part that says write your input stuff here is the input file that you
> would normally use to run NAMD simulation. See the userguide or the
> tutorial for an example of this.
>
> For ADD_YOUR_VALUES_HERE see
> http://www.ks.uiuc.edu/Research/namd/2.8/ug/node73.html
> Good luck.
>
> --Farid
>
> ------------------------------
> *From:* Babban Mia [babbanmia_at_gmail.com]
> *Sent:* Friday, August 12, 2011 1:55 PM
> *To:* Ismail, Mohd F.
>
> *Cc:* Namd Mailing List
> *Subject:* Re: namd-l: Batch Mode MD simulation Script for NAMD
>
> 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=

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:18 CST