Re: Batch Mode MD simulation Script for NAMD

From: Babban Mia (babbanmia_at_gmail.com)
Date: Fri Aug 12 2011 - 05:46:32 CDT

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 pdbwith 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****
>
>

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