From: Deng, Jinxia (Nancy) (jinxianancy.deng_at_zoetis.com)
Date: Tue Dec 08 2015 - 08:43:02 CST
Thank you Jim,
Will give it a try...
Nancy
-----Original Message-----
From: Jim Phillips [mailto:jim_at_ks.uiuc.edu]
Sent: Monday, December 07, 2015 5:43 PM
To: namd-l_at_ks.uiuc.edu; Deng, Jinxia (Nancy)
Subject: Re: namd-l: multiple output .dcd files??
You can do something like this:
for { set ns 50 } { $ns <= 500 } { incr ns 50 } {
dcdfile $output.$ns.dcd
run 25000000
}
Jim
On Mon, 7 Dec 2015, Deng, Jinxia (Nancy) wrote:
> Hi All,
>
> Herein attached the input file for production phase by NAMD.
>
> Wonder whether any one could be very kind to confirm that the current setting is good for 10ps, and the .dcd output has 5 frames with 2ps as frame interval.
>
> If my understanding above is correct, I really want to set up MD task up to 500ns, does that mean the last line should be: "run 250000000"??
>
> If so, is there any way I could specify every 50ns I could have a .dcd file instead of wrapping all trajectory into one file, such as *.50.dcd, *100.dcd......*500.dcd.
>
> I am truly looking forward to any of your response to any piece of this.
>
> Best regards,
>
> Nancy
>
>
>
> Nancy Deng, Ph.D. | Principal Scientist, Computational Chemistry &
> Molecular Modeling Zoetis Inc| Global Therapeutics Research | 333
> Portage Street, Kalamazoo, MI 49007
> Office: 2693599121 | jinxianancy.deng_at_zoetis.com
>
>
>
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