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
>> >
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Feb 18 2010 - 08:00:02 PST
