From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Aug 13 2011 - 08:45:56 CDT
http://www.lmgtfy.com/?q=namd+non+binary+output
On Aug 13, 2011, at 7:36 AM, Babban Mia wrote:
> 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
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