Hi John,
I found something that may be useful. Try this:
awk 'FNR==NR && /TIME/{a[++c] = $6; next} /VDWAALS/{b[++d] = $11} END{for ( i=1;i<=c ;i++) {printf "%s %s\n", a[i],b[i]}}' md.out > summary.VDWAALS
With small changes it can be used for any properties you want.
Adapted from: http://ubuntuforums.org/showthread.php?t=677922
I hope it helps!
Josmar Rocha
--- Em dom, 21/2/10, Carlos Simmerling <carlos.simmerling.gmail.com> escreveu:
> De: Carlos Simmerling <carlos.simmerling.gmail.com>
> Assunto: Re: [AMBER] Script
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Data: Domingo, 21 de Fevereiro de 2010, 11:15
> 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
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >
> _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >>
> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >>
> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
____________________________________________________________________________________
Veja quais são os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 22 2010 - 10:00:03 PST
