Re: Formating of logfile

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 13 2009 - 15:17:49 CST

On Fri, 2009-11-13 at 21:31 +0100, Bjoern Olausson wrote:
> On Fri, Nov 13, 2009 at 19:57, Christi Young <cwhittin_at_mail.usf.edu> wrote:
> > Oh, I think the output file is column, but I make my new file white space. I
> > am not really sure about the output.
> >
> > Christi
> >
> Okay, but then the formating between minimization only (minimization
> ON) and MD/MINI is inconsistent somewhere.
>
> I'll go for white-spaced now and check back when the first error occurs.
> If you have some outputfiles which contain MD and MINI (or maybe a
> repetion of those), could you try to run my script?

bjoern,

i have a stupid question: what is wrong with the "NAMD Plot"
plugin in VMD? why invent another new wheel?

cheers,
   axel.

>
> Find it here:
> http://olausson.de (Posted the latest changes)
> http://olausson.de/attachments/056_anamo.py (direct link)
> (requires python, matplotlib, numpy)
>
>
> Cheers Bjoern
> > On Fri, Nov 13, 2009 at 3:55 AM, Bjoern Olausson <namdlist_at_googlemail.com>
> > wrote:
> >>
> >> On Thursday 12 November 2009 21:07:56 you wrote:
> >> > On Wed, Nov 11, 2009 at 8:07 AM, Bjoern Olausson
> >> <namdlist_at_googlemail.com>wrote:
> >> > > Ha namd users,
> >> > >
> >> > > can anybody tell me the formating of the output file, especially the
> >> > > formatting of the following lines:
> >> > >
> >> > > PRESSURE:
> >> > > GPRESSURE:
> >> > > PRESSAVG:
> >> > > GPRESSAVG:
> >> > > ENERGY:
> >> > >
> >> > > Are the values in fixed columns or white space separated? Or is there
> >> > > any
> >> > > criteria which can separate these values for 100%
> >> > >
> >> > > I used the following python synthax to extract the values, but today
> >> > > it
> >> > > failed
> >> > > for th first time because the formatting did no longer match:
> >> > >
> >> > > def Energy(line) :
> >> > > TS.append(int(line[7:16].strip()))
> >> > > BOND.append(float(line[16:31].strip()))
> >> > > ANGLE.append(float(line[31:46].strip()))
> >> > > DIHED.append(float(line[46:61].strip()))
> >> > > IMPRP.append(float(line[61:76].strip()))
> >> > > ELECT.append(float(line[76:96].strip()))
> >> > > VDW.append(float(line[96:112].strip()))
> >> > > BOUNDARY.append(float(line[112:126].strip()))
> >> > > MISC.append(float(line[126:141].strip()))
> >> > > KINETIC.append(float(line[141:156].strip()))
> >> > > TOTAL.append(float(line[156:176].strip()))
> >> > > TEMP.append(float(line[176:191].strip()))
> >> > > TOTAL2.append(float(line[191:206].strip()))
> >> > > TOTAL3.append(float(line[206:221].strip()))
> >> > > TEMPAVG.append(float(line[221:236].strip()))
> >> > > # If "minimization on" was used these values are not populated
> >> > > if not MINo :
> >> > > PRESSURE.append(float(line[236:256].strip()))
> >> > > GPRESSURE.append(float(line[256:271].strip()))
> >> > > VOLUME.append(float(line[271:286].strip()))
> >> > > PRESSAVG.append(float(line[286:301].strip()))
> >> > > GPRESSAVG.append(float(line[301:316].strip()))
> >> > >
> >> > > kind regards
> >> > > Bjoern
> >> > >
> >> > awk '/^ENERGY/ {print $2 " " $12}' ./output > ./newfile
> >> >
> >> > to separate timestep and pot en. It is all one line per timestep or
> >> > title.
> >> > Hope this helps.
> >> >
> >> > Christi Young
> >> >
> >>
> >> Your answer implies that the lines are "white space" separated.
> >> Are you sure about it? Would make life easier if you are right. *G*
> >>
> >> Ah, whatever, I'll go for "white spaced" and use it until it fails some
> >> day,
> >> then I know for sure :-)
> >>
> >> Cheers
> >> Bjoern
> >>
> >> --
> >> Bjoern Olausson
> >> Martin-Luther-Universit├Ąt Halle-Wittenberg
> >> Fachbereich Biochemie/Biotechnologie
> >> Kurt-Mothes-Str. 3
> >> 06120 Halle/Saale
> >>
> >> Phone: +49-345-55-24942
> >
> >
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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