Re: Batch Mode MD simulation Script for NAMD

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 12 2011 - 07:53:13 CDT

On Fri, Aug 12, 2011 at 7:45 AM, Jeffrey Potoff
<jpotoff_at_chem1.eng.wayne.edu> wrote:
> Have you read the users guide for NAMD?
>
> http://www.ks.uiuc.edu/Research/namd/2.8/ug/node13.html
>
> It is trivial to output data every 1ps to a DCD file.† From the DCD file you
> can use VMD to extract whatever information you like, such as the
> coordinates in PDB format.

add to that the fact that it is actually not a very smart move to analyze
a trajectory in pdb format for two reasons. a) it takes _much_ more time
and disk space to read and parse pdb format files and b) in pdb format
coordinates are stored with truncated precision, so any results are tainted
by arbitrary truncation.

in general, it is a wrong to assume the work flow for one MD code
is like for another, particularly comparing a rather old fashioned code
with a more newer implementation.

axel

>
> On 8/12/2011 6:46 AM, Babban Mia wrote:
>
> 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
>
>
> --
> ======================================================================
> Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
> Associate Professor Wayne State University
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> Detroit, MI 48202 Fax: (313)578-5815
> http://potoff1.eng.wayne.edu
> ======================================================================
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.comhttp://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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