Re: Batch Mode MD simulation Script for NAMD

From: Jernej Zidar (jernej.zidar_at_gmail.com)
Date: Fri Aug 12 2011 - 08:03:21 CDT

I have yet to start my production simulations in NAMD, but I will surely use the restart facilities offered by NAMD, for the simulations are going to quite long and the maximum job time on the cluster is three days.

In any a DCD trajectory is THE way to go for further analysis.

Best,
Jernej

On 12. avg. 2011, at 20:53, Axel Kohlmeyer wrote:

> 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.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>

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