From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Fri Nov 13 2009 - 14:31:22 CST
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?
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-Universität Halle-Wittenberg
>> Fachbereich Biochemie/Biotechnologie
>> Kurt-Mothes-Str. 3
>> 06120 Halle/Saale
>>
>> Phone: +49-345-55-24942
>
>
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