Re: Batch Mode MD simulation Script for NAMD

From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Fri Aug 12 2011 - 06:45:12 CDT

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.

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
> <mailto: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>
> [mailto: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 <mailto: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
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