you could have a simple script that pulls the VDW to one file, TIME to
another, then uses unix "paste" to combine them.
On Thu, Feb 18, 2010 at 10:43 AM, Lachele Foley (Lists)
<lf.list.gmail.com>wrote:
> There isn't an easy one-liner. At this point, you probably need to
> learn awk or perl if you want to be fancy and efficient. That's what
> we do.
>
> Or, you could run Carlos' one-liner twice, once for TIME and once for
> VDWAALS (understanding that some will be averages or rms, etc.), then
> import the columns into a spreadsheet, etc.
>
> To get only averages, maybe try something like "grep -A8 "A V E R A G
> E S O V E R" file.o > tempfile.o" then use the one-liner (or pipe
> directly into the one-liner if you know how).
>
>
>
> On Thu, Feb 18, 2010 at 8:15 AM, Beale, John <John.Beale.stlcop.edu>
> wrote:
> > 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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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
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> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Sun Feb 21 2010 - 06:30:02 PST
