RE: [AMBER] Script

From: Beale, John <John.Beale.stlcop.edu>
Date: Thu, 18 Feb 2010 07:15:59 -0600

OK, that worked fine. One more thing: is there a convenient way to pair
each of the VDWAALS points with the time in the simulation so that I can
plot VDW vs. time?

Thanks!

John

-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
Behalf Of Carlos Simmerling
Sent: Thursday, February 18, 2010 6:59 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Script

adjust the number in the awk part- that tells it what column to print,

On Thu, Feb 18, 2010 at 7:47 AM, Beale, John <John.Beale.stlcop.edu>
wrote:

> Hi Carlos,
>
> I tried using grep and awk as you suggested. The vdw.data file that I
> get has just a column of equal signs running down the left side of the
> page. Any ideas?
>
> Thanks!
>
> John
>
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Carlos Simmerling
> Sent: Thursday, February 18, 2010 6:41 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Script
>
> hi john-
> do you have an existing MD output, or want to postprocess something?
> if existing output, I've found that using grep and awk are easiest for
> me.
>
> for example:
>
> grep VDWAALS md.out | awk '{print $3}' > vdw.data
>
>
> On Thu, Feb 18, 2010 at 7:35 AM, Beale, John <John.Beale.stlcop.edu>
> wrote:
>
> > I am hoping that someone will be willing to help me. I am just
> learning
> > to write scripts and what I need to do is beyond me for right now. I
> am
> > using the script "process_mdout.perl". I would like to modify this
> > script so that it outputs VDWAALS energy over the trajectory of an
MD
> > simulation. I would be grateful if someone could modify the script
to
> do
> > this and post it or send it to me. Thanks!
> >
> >
> >
> > John M. Beale, Ph,D,
> >
> > Associate Professor of Medicinal Chemistry
> >
> > St. Louis College of Pharmacy
> >
> > 4588 Parkview Place
> >
> > St. Louis, Missouri 63110
> >
> > (314)-446-8461
> >
> > Cell: (314)-315-0409
> >
> > FAX (314) 446-8460
> >
> > jbeale.stlcop.edu
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
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Received on Thu Feb 18 2010 - 05:30:03 PST
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