Dear Alavi:
You should specify the vdW radii (of iron) in ESP charge calculation by
pop=(mk,readradii).
This paper may contain the vdW radii (and well depth for later MM
calculation) of Fe2+: DOI: 10.1021/jp054177x. But use it carefully.
Best Regards,
WANG, Ruixing
END
2016-02-02 4:00 GMT+08:00 amber-request.ambermd.org <
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Wrong or no center in RdPar. (Fatemeh Sadat Alavi )
> 2. Replacement for xmgrace (Jean-Patrick Francoia)
> 3. Re: Replacement for xmgrace (Andrea Spitaleri)
> 4. Re: Replacement for xmgrace (Hannes Loeffler)
> 5. Re: Replacement for xmgrace (Jean-Patrick Francoia)
> 6. Re: Replacement for xmgrace (Vasantha Kumar)
> 7. Re: Replacement for xmgrace (Bill Ross)
> 8. Re: Replacement for xmgrace (Lorenzo Gontrani)
> 9. Re: Replacement for xmgrace (David A Case)
> 10. Re: 3DRISM: erratic values for partial molar volume
> (Josh Berryman)
> 11. Re: Replacement for xmgrace (Jean-Patrick Francoia)
> 12. Re: Replacement for xmgrace (Jason Swails)
> 13. Re: Wrong or no center in RdPar. (Jason Swails)
> 14. Re: Replacement for xmgrace (Jean-Patrick Francoia)
> 15. Re: Replacement for xmgrace (Jason Swails)
> 16. Re: Replacement for xmgrace (Jean-Patrick Francoia)
> 17. Re: Replacement for xmgrace (Jason Swails)
> 18. Re: Replacement for xmgrace (Hai Nguyen)
> 19. Re: Replacement for xmgrace (Jean-Patrick Francoia)
> 20. Re: Replacement for xmgrace (Hai Nguyen)
> 21. Value of ntrx=7 (Krantzman, Kristin D)
> 22. Re: Replacement for xmgrace (Jason Swails)
> 23. Re: Value of ntrx=7 (Jason Swails)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 01 Feb 2016 09:55:38 +0330
> From: "Fatemeh Sadat Alavi " <f_alavi.sbu.ac.ir>
> Subject: [AMBER] Wrong or no center in RdPar.
> To: "amber" <AMBER.ambermd.org>
> Message-ID: <WC20160201062538.98027F.sbu.ac.ir>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi
> I have one question about doing MM in gaussian with amber method.
> my structure has iron, I calculated ESP charge and made .frcmod by
> antechamber until put them in the end of input file for MM setup( to
> complete missing parameter).
> but I have this error:
> Read MM parameter file:
> Define FE 1
> Define CD 2
> Wrong or no center in RdPar.
> Error termination via Lnk1e in /share/apps/g09d/g09/l101.exe
>
> can you help me?
> thanks a lot
> Best regards
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 1 Feb 2016 10:48:31 +0100
> From: Jean-Patrick Francoia <jeanpatrick.francoia.gmail.com>
> Subject: [AMBER] Replacement for xmgrace
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <56AF29EF.2050500.gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hi,
>
> Just a quick question. Is there a better (meaning: more recent) program
> than xmgrace to analyse the outputs of MD ? Preferably one that runs on
> Linux.
>
> Thanks
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 1 Feb 2016 10:52:01 +0100
> From: Andrea Spitaleri <andrea.spitaleri.iit.it>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: amber.ambermd.org
> Message-ID: <56AF2AC1.4040809.iit.it>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hi,
> what about gnuplot? easy, quick and runnable in script.
>
> HTH
>
> and
>
> On 01/02/2016 10:48, Jean-Patrick Francoia wrote:
> > Hi,
> >
> > Just a quick question. Is there a better (meaning: more recent) program
> > than xmgrace to analyse the outputs of MD ? Preferably one that runs on
> > Linux.
> >
> > Thanks
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Andrea Spitaleri PhD
> Istituto Computational mOdelling of NanosCalE and bioPhysical sysTems -
> CONCEPT LabItaliano di Tecnologia
> Via Morego, 30 16163 Genova
> cell: +39 3485188790
> http://www.iit.it/en/d3-people/andrea-spitaleri.html
> ORCID: http://orcid.org/0000-0003-3012-3557
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 1 Feb 2016 10:13:11 +0000
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: <amber.ambermd.org>
> Message-ID: <20160201101311.7d764263.zgb83773vig.dl.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> Why would a "less" recent program (whatever you mean by this) be better
> than a "more" recent one? What does Grace not do that you would want
> to see in another program?
>
> On Mon, 1 Feb 2016 10:48:31 +0100
> Jean-Patrick Francoia <jeanpatrick.francoia.gmail.com> wrote:
>
> > Hi,
> >
> > Just a quick question. Is there a better (meaning: more recent)
> > program than xmgrace to analyse the outputs of MD ? Preferably one
> > that runs on Linux.
> >
> > Thanks
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 1 Feb 2016 11:17:42 +0100
> From: Jean-Patrick Francoia <jeanpatrick.francoia.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: amber.ambermd.org
> Message-ID: <56AF30C6.7030708.gmail.com>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Thank you, that's perfect. I didn't know gnuplot can do that.
>
> Le 01/02/2016 10:52, Andrea Spitaleri a ?crit :
> > Hi,
> > what about gnuplot? easy, quick and runnable in script.
> >
> > HTH
> >
> > and
> >
> > On 01/02/2016 10:48, Jean-Patrick Francoia wrote:
> >> Hi,
> >>
> >> Just a quick question. Is there a better (meaning: more recent) program
> >> than xmgrace to analyse the outputs of MD ? Preferably one that runs on
> >> Linux.
> >>
> >> Thanks
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 1 Feb 2016 11:51:52 +0100
> From: Vasantha Kumar <vin.vasanth.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAKY45+vqJv+GU0gy4W6ToNJh9DTLo99xsdcze2v1fYwqYGMf=
> g.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi...
>
> As compared to gnuplot, "xmgrace" is good to perform quick checks on your
> results. gnuplot is very good to plot final results and every time it
> requires little bit formatting to handle AMBER output files.
>
> Ciao
> Vasantha
>
> 2016-02-01 11:17 GMT+01:00 Jean-Patrick Francoia <
> jeanpatrick.francoia.gmail.com>:
>
> > Thank you, that's perfect. I didn't know gnuplot can do that.
> >
> > Le 01/02/2016 10:52, Andrea Spitaleri a ?crit :
> > > Hi,
> > > what about gnuplot? easy, quick and runnable in script.
> > >
> > > HTH
> > >
> > > and
> > >
> > > On 01/02/2016 10:48, Jean-Patrick Francoia wrote:
> > >> Hi,
> > >>
> > >> Just a quick question. Is there a better (meaning: more recent)
> program
> > >> than xmgrace to analyse the outputs of MD ? Preferably one that runs
> on
> > >> Linux.
> > >>
> > >> Thanks
> > >>
> > >> _______________________________________________
> > >> 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
> >
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 1 Feb 2016 02:58:55 -0800
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <56AF3A6F.6040600.cgl.ucsf.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Can you write a script to prepare the amber output for gnuplot?
>
> Bill
>
> On 2/1/16 2:51 AM, Vasantha Kumar wrote:
> > Hi...
> >
> > As compared to gnuplot, "xmgrace" is good to perform quick checks on
> your
> > results. gnuplot is very good to plot final results and every time it
> > requires little bit formatting to handle AMBER output files.
> >
> > Ciao
> > Vasantha
> >
> > 2016-02-01 11:17 GMT+01:00 Jean-Patrick Francoia <
> > jeanpatrick.francoia.gmail.com>:
> >
> >> Thank you, that's perfect. I didn't know gnuplot can do that.
> >>
> >> Le 01/02/2016 10:52, Andrea Spitaleri a ?crit :
> >>> Hi,
> >>> what about gnuplot? easy, quick and runnable in script.
> >>>
> >>> HTH
> >>>
> >>> and
> >>>
> >>> On 01/02/2016 10:48, Jean-Patrick Francoia wrote:
> >>>> Hi,
> >>>>
> >>>> Just a quick question. Is there a better (meaning: more recent)
> program
> >>>> than xmgrace to analyse the outputs of MD ? Preferably one that runs
> on
> >>>> Linux.
> >>>>
> >>>> Thanks
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 1 Feb 2016 12:26:39 +0100
> From: Lorenzo Gontrani <lorenzo.gontrani.uniroma1.it>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: amber.ambermd.org
> Message-ID: <56AF40EF.3050407.uniroma1.it>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> xmgrace is great..and lightweight. But you can try qtiplot, if you
> prefer an origin-like environment
>
> Lorenzo
>
> On 02/01/2016 10:48 AM, Jean-Patrick Francoia wrote:
> > Hi,
> >
> > Just a quick question. Is there a better (meaning: more recent) program
> > than xmgrace to analyse the outputs of MD ? Preferably one that runs on
> > Linux.
> >
> > Thanks
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> ==========================================
> Lorenzo Gontrani
> Research associate - EDXD group
> University of Rome "La Sapienza"
> ResearcherID: L-6061-2014
>
> GSM +39 338 7615798
> Email lorenzo DOT gontrani AT uniroma1 DOT it
> Webpage: http://webcaminiti/gontrani.html
> =========================================
> Rispetta l'ambiente: se non ? necessario, non stampare
> questa e-mail
> Protect the environment: do not print this e-mail, unless
> necessary
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Mon, 1 Feb 2016 08:08:48 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20160201130848.GA24385.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Mon, Feb 01, 2016, Lorenzo Gontrani wrote:
>
> > xmgrace is great..and lightweight.
>
> Just some (off-topic) comments about why I like xmgrace:
>
> 1. Plots generally look good and can be interactively edited if they don't.
> Consider modifying your ~/.grace/templates/Default.agr file to specify
> Helvetica as "font 0" (the default) and change 'xaxis label char size' to
> 1.25
> (from 1.0); same for yaxis.
>
> 2. A single .agr file has both the data and the formatting in a single
> file.
> This is good if you come back months or years later and don't remember your
> file naming conventions.
>
> 3. You can also write simple scripts to systematically modify lots of
> files, to replace the data but keep the formatting, etc. Once you grok the
> file syntax (which is pretty straightforward), it's about as easy to write
> scripts to create or manipulate xmgrace files as it is to write gnuplot or
> matplotlib scripts.
>
> 4. Consider aliasing xmgrace to 'xmgrace -hdevice PDF'. This means that
> "print" will create a PDF file (rather than the default PostScript). This
> is
> likely to be what most people want.
>
> ....dac
>
> (OK: I realize I've probably started a flame war here... Next up: why you
> should write all your code in LISP.)
>
>
>
> ------------------------------
>
> Message: 10
> Date: Mon, 1 Feb 2016 14:16:01 +0100
> From: Josh Berryman <the.real.josh.berryman.gmail.com>
> Subject: Re: [AMBER] 3DRISM: erratic values for partial molar volume
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CANRE9HWtMVT-tczhg4ABbTZVNtNfZNyE4y_hAuKvJD7-LvXkEA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Replying to list for the record (I sent structs and inputs to Tyler and
> Dave so they could have a look, some helpful discussion followed).
>
> 1) 3D RISM energies can be very sensitive to conformation, especially at
> high concentrations of multiple species in the solvent, and especially with
> cavities or odd-shaped surfaces in the solute. This is not entirely a bad
> thing and might be at least somewhat physical, but is a pitfall when doing
> single-point energy evaluation of structures generated with other means
> such as GBSA.
>
> 2) Sampling with MD-RISM is manageable and avoids massive jumps in energy:
> the potential surface described is at least somewhat smooth in the
> valleys. If minimisations or singlepoint energy evaluations are behaving
> suspiciously, my takehome from this is to just pick the lowest-energy snap
> and do MD from it as a starting point.
>
> I got (apparently) adequate results using this input file, simplified
> somewhat from the one in the manual as I wanted to avoid multiplying my
> problems with too much novelty:
>
> comment here
>
> &cntrl
>
> ntx=1, ntpr=10, ntwx=10, ntwr=10, nstlim=2000, dt=0.001,
>
> ntt=3, tempi=300, temp0=300, gamma_ln=10., ig=3233, !Langevin MD
>
> ntb=0,
> !Non-periodic
>
> cut=999., !solute-solute interactions
>
> irism=1,
>
> /
>
> &rism
>
> rismnrespa=2,
>
> fcestride=0,fcecrd=2,
>
> /
>
> "RISM! You have it or you don't, that's a fallacy" .... Gorrillaz, Clint
> Eastwood.
>
> Josh
>
>
>
>
>
>
>
>
> On 27 January 2016 at 11:05, Josh Berryman <
> the.real.josh.berryman.gmail.com
> > wrote:
>
> > Hello RISM experts,
> >
> > I am running 3DRISM calculations on snaps taken from an MD run, to try
> and
> > estimate solvation energy. The snaps were slightly altered after the MD
> > (extra proton, appropriate change to .top file, followed by minimise in
> > Generalised Born with heavy atoms restrained).
> >
> > I'm using an .xvv for SPC water with 1M of Cl- ions present. The peptide
> > has net positive charge.
> >
> > GB energy is well-behaved, but I get wildly different RISM energies (100s
> > kcal/mol) for different groups of very similar-looking snaps, this is
> > traceable to specific terms in the output:
> >
> > --solvent PE
> > --Partial Molar Volume
> > --dcf Integral
> >
> > Kirkwood-Buff is not affected, it is fairly smooth.
> >
> > What could cause such big changes in the PMV terms? I don't see anything
> > special by plotting out the volumetric info although I am not an expert.
> >
> > I'm cautious about just going ahead and do a RISM minimise because the
> > outliers are *down* in energy from the main bulk of the snaps (and its
> > expensive, of course).
> >
> > Josh
> >
> > **********************************************
> >
> > Input file is pretty standard afaik:
> > &cntrl
> >
> > ntx=1, ntpr=1, ntwx=1,
> >
> > imin=5, maxcyc=1, !Single-point energy calculation
> >
> > ntb=0, !Non-periodic
> >
> > cut=9999., !solute-solute interactions
> >
> > irism=1,
> >
> > /
> >
> > &rism
> >
> > tolerance=1e-4, !1e-4 Saves some time compared to 1e-5
> >
> > apply_rism_force=0, !Saves some time.
> >
> > npropagate=1, !Saves some time and 4*8*Nbox bytes
> >
> > ntwrism=1,
> >
> > write_thermo=1,
> >
> > /
> >
> >
>
>
> ------------------------------
>
> Message: 11
> Date: Mon, 1 Feb 2016 14:57:41 +0100
> From: Jean-Patrick Francoia <jeanpatrick.francoia.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: amber.ambermd.org
> Message-ID: <56AF6455.1090808.gmail.com>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> "Plots generally look good"...Yeah maybe with a little formatting as you
> suggested. Actually xmgrace has an old look on my platform, a bit like
> xleap. That's why I will go for gnuplot.
>
> I had a bit of spare time, so I wrote a quick script:
>
> #!/usr/bin/python
> # coding: utf-8
>
> help = """Plot.py
>
> Script to plot (x, y) data from files
>
> Usage:
> plot.py <files>...
>
> Options:
> -h --help Display help
> """
>
>
> from docopt import docopt
> import matplotlib.pyplot as plt
>
> plt.style.use('ggplot')
> plt.style.use('seaborn-poster')
> plt.tick_params(left='off', bottom='off', top='off', right='off')
>
>
> arguments = docopt(help)
>
> for arg in arguments['<files>']:
> pts_x = []
> pts_y = []
>
> with open(arg, 'r') as f:
> for line in f.readlines():
> res = [float(value.strip()) for value in line.split(' ')
> if value.strip() != '']
> if res:
> pts_x.append(res[0])
> pts_y.append(res[1])
>
> plt.plot(pts_x, pts_y, label=arg)
>
> plt.legend()
> plt.show()
>
> Just to try docopt and the new version of matplotlib (which includes
> styles). The graph formatting is clearly R-inspired (the devs of
> matplotlib finally underestood...).
>
> Usage:
> ./plot.py summary.EPTOT summary.ETOT
>
> Result:
> http://i.imgur.com/FPdBfsz.png
>
> Le 01/02/2016 14:08, David A Case a ?crit :
> > On Mon, Feb 01, 2016, Lorenzo Gontrani wrote:
> >
> >> xmgrace is great..and lightweight.
> > Just some (off-topic) comments about why I like xmgrace:
> >
> > 1. Plots generally look good and can be interactively edited if they
> don't.
> > Consider modifying your ~/.grace/templates/Default.agr file to specify
> > Helvetica as "font 0" (the default) and change 'xaxis label char size'
> to 1.25
> > (from 1.0); same for yaxis.
> >
> > 2. A single .agr file has both the data and the formatting in a single
> file.
> > This is good if you come back months or years later and don't remember
> your
> > file naming conventions.
> >
> > 3. You can also write simple scripts to systematically modify lots of
> > files, to replace the data but keep the formatting, etc. Once you grok
> the
> > file syntax (which is pretty straightforward), it's about as easy to
> write
> > scripts to create or manipulate xmgrace files as it is to write gnuplot
> or
> > matplotlib scripts.
> >
> > 4. Consider aliasing xmgrace to 'xmgrace -hdevice PDF'. This means that
> > "print" will create a PDF file (rather than the default PostScript).
> This is
> > likely to be what most people want.
> >
> > ....dac
> >
> > (OK: I realize I've probably started a flame war here... Next up: why you
> > should write all your code in LISP.)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 12
> Date: Mon, 1 Feb 2016 09:05:48 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3regJVNHTEfzM1rw12KzEz+E+hcizF2EDXOJDL=
> cd+h+Q.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> If you're trying to plot data from mdout files, you can always try
> "mdout_analyzer.py". It's built on top of matplotlib and doesn't require
> any pre-processing step for mdout files (i.e., you can just type:
>
> mdout_analyzer.py mdout1 mdout2 ... mdoutN
> )
>
> HTH,
> Jason
>
> On Mon, Feb 1, 2016 at 8:57 AM, Jean-Patrick Francoia <
> jeanpatrick.francoia.gmail.com> wrote:
>
> > "Plots generally look good"...Yeah maybe with a little formatting as you
> > suggested. Actually xmgrace has an old look on my platform, a bit like
> > xleap. That's why I will go for gnuplot.
> >
> > I had a bit of spare time, so I wrote a quick script:
> >
> > #!/usr/bin/python
> > # coding: utf-8
> >
> > help = """Plot.py
> >
> > Script to plot (x, y) data from files
> >
> > Usage:
> > plot.py <files>...
> >
> > Options:
> > -h --help Display help
> > """
> >
> >
> > from docopt import docopt
> > import matplotlib.pyplot as plt
> >
> > plt.style.use('ggplot')
> > plt.style.use('seaborn-poster')
> > plt.tick_params(left='off', bottom='off', top='off', right='off')
> >
> >
> > arguments = docopt(help)
> >
> > for arg in arguments['<files>']:
> > pts_x = []
> > pts_y = []
> >
> > with open(arg, 'r') as f:
> > for line in f.readlines():
> > res = [float(value.strip()) for value in line.split(' ')
> > if value.strip() != '']
> > if res:
> > pts_x.append(res[0])
> > pts_y.append(res[1])
> >
> > plt.plot(pts_x, pts_y, label=arg)
> >
> > plt.legend()
> > plt.show()
> >
> > Just to try docopt and the new version of matplotlib (which includes
> > styles). The graph formatting is clearly R-inspired (the devs of
> > matplotlib finally underestood...).
> >
> > Usage:
> > ./plot.py summary.EPTOT summary.ETOT
> >
> > Result:
> > http://i.imgur.com/FPdBfsz.png
> >
> > Le 01/02/2016 14:08, David A Case a ?crit :
> > > On Mon, Feb 01, 2016, Lorenzo Gontrani wrote:
> > >
> > >> xmgrace is great..and lightweight.
> > > Just some (off-topic) comments about why I like xmgrace:
> > >
> > > 1. Plots generally look good and can be interactively edited if they
> > don't.
> > > Consider modifying your ~/.grace/templates/Default.agr file to specify
> > > Helvetica as "font 0" (the default) and change 'xaxis label char size'
> > to 1.25
> > > (from 1.0); same for yaxis.
> > >
> > > 2. A single .agr file has both the data and the formatting in a single
> > file.
> > > This is good if you come back months or years later and don't remember
> > your
> > > file naming conventions.
> > >
> > > 3. You can also write simple scripts to systematically modify lots of
> > > files, to replace the data but keep the formatting, etc. Once you grok
> > the
> > > file syntax (which is pretty straightforward), it's about as easy to
> > write
> > > scripts to create or manipulate xmgrace files as it is to write gnuplot
> > or
> > > matplotlib scripts.
> > >
> > > 4. Consider aliasing xmgrace to 'xmgrace -hdevice PDF'. This means
> that
> > > "print" will create a PDF file (rather than the default PostScript).
> > This is
> > > likely to be what most people want.
> > >
> > > ....dac
> > >
> > > (OK: I realize I've probably started a flame war here... Next up: why
> you
> > > should write all your code in LISP.)
> > >
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 13
> Date: Mon, 1 Feb 2016 09:08:54 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Wrong or no center in RdPar.
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAEk9e3r9gq0jgbtwO8qwVdmDUJBtScxRXTdSQU9s8qDZmzFaAw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Feb 1, 2016 at 1:25 AM, Fatemeh Sadat Alavi <f_alavi.sbu.ac.ir>
> wrote:
>
> > Hi
> > I have one question about doing MM in gaussian with amber method.
> > my structure has iron, I calculated ESP charge and made .frcmod by
> > antechamber until put them in the end of input file for MM setup( to
> > complete missing parameter).
> > but I have this error:
> > Read MM parameter file:
> > Define FE 1
> > Define CD 2
> > Wrong or no center in RdPar.
> > Error termination via Lnk1e in /share/apps/g09d/g09/l101.exe
> >
>
> ?It seems like you are trying to run the MD within Gaussian itself? If so,
> this is the wrong list to ask that question. Most of the experts here know
> how to use Amber to run dynamics and would have little use for running
> dynamics with Gaussian. Note, you can run MD with sander and use Gaussian
> for the QM part through an external interface -- you can always try that if
> you want to.
>
> I suggest trying the Gaussian help instead, wherever that might be.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 14
> Date: Mon, 1 Feb 2016 15:32:41 +0100
> From: Jean-Patrick Francoia <jeanpatrick.francoia.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <56AF6C89.6000001.gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Cool.
>
> It's buggy however:
>
> Traceback (most recent call last):
> File "/home/djipey/SOFT/amber14/bin/mdout_analyzer.py", line 63, in
> <module>
> mdout = MdoutClass(f)
> File
>
> "/home/djipey/SOFT/amber14/lib/python2.7/site-packages/mdoutanalyzer/mdout.py",
> line 82, in __init__
> if self.properties['imin'] == 5:
> KeyError: 'imin'
>
> Le 01/02/2016 15:05, Jason Swails a ?crit :
> > If you're trying to plot data from mdout files, you can always try
> > "mdout_analyzer.py". It's built on top of matplotlib and doesn't require
> > any pre-processing step for mdout files (i.e., you can just type:
> >
> > mdout_analyzer.py mdout1 mdout2 ... mdoutN
> > )
> >
> > HTH,
> > Jason
> >
> > On Mon, Feb 1, 2016 at 8:57 AM, Jean-Patrick Francoia <
> > jeanpatrick.francoia.gmail.com> wrote:
> >
> >> "Plots generally look good"...Yeah maybe with a little formatting as you
> >> suggested. Actually xmgrace has an old look on my platform, a bit like
> >> xleap. That's why I will go for gnuplot.
> >>
> >> I had a bit of spare time, so I wrote a quick script:
> >>
> >> #!/usr/bin/python
> >> # coding: utf-8
> >>
> >> help = """Plot.py
> >>
> >> Script to plot (x, y) data from files
> >>
> >> Usage:
> >> plot.py <files>...
> >>
> >> Options:
> >> -h --help Display help
> >> """
> >>
> >>
> >> from docopt import docopt
> >> import matplotlib.pyplot as plt
> >>
> >> plt.style.use('ggplot')
> >> plt.style.use('seaborn-poster')
> >> plt.tick_params(left='off', bottom='off', top='off', right='off')
> >>
> >>
> >> arguments = docopt(help)
> >>
> >> for arg in arguments['<files>']:
> >> pts_x = []
> >> pts_y = []
> >>
> >> with open(arg, 'r') as f:
> >> for line in f.readlines():
> >> res = [float(value.strip()) for value in line.split(' ')
> >> if value.strip() != '']
> >> if res:
> >> pts_x.append(res[0])
> >> pts_y.append(res[1])
> >>
> >> plt.plot(pts_x, pts_y, label=arg)
> >>
> >> plt.legend()
> >> plt.show()
> >>
> >> Just to try docopt and the new version of matplotlib (which includes
> >> styles). The graph formatting is clearly R-inspired (the devs of
> >> matplotlib finally underestood...).
> >>
> >> Usage:
> >> ./plot.py summary.EPTOT summary.ETOT
> >>
> >> Result:
> >> http://i.imgur.com/FPdBfsz.png
> >>
> >> Le 01/02/2016 14:08, David A Case a ?crit :
> >>> On Mon, Feb 01, 2016, Lorenzo Gontrani wrote:
> >>>
> >>>> xmgrace is great..and lightweight.
> >>> Just some (off-topic) comments about why I like xmgrace:
> >>>
> >>> 1. Plots generally look good and can be interactively edited if they
> >> don't.
> >>> Consider modifying your ~/.grace/templates/Default.agr file to specify
> >>> Helvetica as "font 0" (the default) and change 'xaxis label char size'
> >> to 1.25
> >>> (from 1.0); same for yaxis.
> >>>
> >>> 2. A single .agr file has both the data and the formatting in a single
> >> file.
> >>> This is good if you come back months or years later and don't remember
> >> your
> >>> file naming conventions.
> >>>
> >>> 3. You can also write simple scripts to systematically modify lots of
> >>> files, to replace the data but keep the formatting, etc. Once you grok
> >> the
> >>> file syntax (which is pretty straightforward), it's about as easy to
> >> write
> >>> scripts to create or manipulate xmgrace files as it is to write gnuplot
> >> or
> >>> matplotlib scripts.
> >>>
> >>> 4. Consider aliasing xmgrace to 'xmgrace -hdevice PDF'. This means
> that
> >>> "print" will create a PDF file (rather than the default PostScript).
> >> This is
> >>> likely to be what most people want.
> >>>
> >>> ....dac
> >>>
> >>> (OK: I realize I've probably started a flame war here... Next up: why
> you
> >>> should write all your code in LISP.)
> >>>
> >>> _______________________________________________
> >>> 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
> >>
> >
> >
>
>
>
>
> ------------------------------
>
> Message: 15
> Date: Mon, 1 Feb 2016 09:36:39 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAEk9e3qiK-G2ZjkJQZbebNaatP2HLYf+8t0OCMGqNokuSxFdAQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Can you provide the mdout file that failed here?
>
> On Mon, Feb 1, 2016 at 9:32 AM, Jean-Patrick Francoia <
> jeanpatrick.francoia.gmail.com> wrote:
>
> > Cool.
> >
> > It's buggy however:
> >
> > Traceback (most recent call last):
> > File "/home/djipey/SOFT/amber14/bin/mdout_analyzer.py", line 63, in
> > <module>
> > mdout = MdoutClass(f)
> > File
> >
> >
> "/home/djipey/SOFT/amber14/lib/python2.7/site-packages/mdoutanalyzer/mdout.py",
> > line 82, in __init__
> > if self.properties['imin'] == 5:
> > KeyError: 'imin'
> >
> > Le 01/02/2016 15:05, Jason Swails a ?crit :
> > > If you're trying to plot data from mdout files, you can always try
> > > "mdout_analyzer.py". It's built on top of matplotlib and doesn't
> require
> > > any pre-processing step for mdout files (i.e., you can just type:
> > >
> > > mdout_analyzer.py mdout1 mdout2 ... mdoutN
> > > )
> > >
> > > HTH,
> > > Jason
> > >
> > > On Mon, Feb 1, 2016 at 8:57 AM, Jean-Patrick Francoia <
> > > jeanpatrick.francoia.gmail.com> wrote:
> > >
> > >> "Plots generally look good"...Yeah maybe with a little formatting as
> you
> > >> suggested. Actually xmgrace has an old look on my platform, a bit like
> > >> xleap. That's why I will go for gnuplot.
> > >>
> > >> I had a bit of spare time, so I wrote a quick script:
> > >>
> > >> #!/usr/bin/python
> > >> # coding: utf-8
> > >>
> > >> help = """Plot.py
> > >>
> > >> Script to plot (x, y) data from files
> > >>
> > >> Usage:
> > >> plot.py <files>...
> > >>
> > >> Options:
> > >> -h --help Display help
> > >> """
> > >>
> > >>
> > >> from docopt import docopt
> > >> import matplotlib.pyplot as plt
> > >>
> > >> plt.style.use('ggplot')
> > >> plt.style.use('seaborn-poster')
> > >> plt.tick_params(left='off', bottom='off', top='off', right='off')
> > >>
> > >>
> > >> arguments = docopt(help)
> > >>
> > >> for arg in arguments['<files>']:
> > >> pts_x = []
> > >> pts_y = []
> > >>
> > >> with open(arg, 'r') as f:
> > >> for line in f.readlines():
> > >> res = [float(value.strip()) for value in line.split(' ')
> > >> if value.strip() != '']
> > >> if res:
> > >> pts_x.append(res[0])
> > >> pts_y.append(res[1])
> > >>
> > >> plt.plot(pts_x, pts_y, label=arg)
> > >>
> > >> plt.legend()
> > >> plt.show()
> > >>
> > >> Just to try docopt and the new version of matplotlib (which includes
> > >> styles). The graph formatting is clearly R-inspired (the devs of
> > >> matplotlib finally underestood...).
> > >>
> > >> Usage:
> > >> ./plot.py summary.EPTOT summary.ETOT
> > >>
> > >> Result:
> > >> http://i.imgur.com/FPdBfsz.png
> > >>
> > >> Le 01/02/2016 14:08, David A Case a ?crit :
> > >>> On Mon, Feb 01, 2016, Lorenzo Gontrani wrote:
> > >>>
> > >>>> xmgrace is great..and lightweight.
> > >>> Just some (off-topic) comments about why I like xmgrace:
> > >>>
> > >>> 1. Plots generally look good and can be interactively edited if they
> > >> don't.
> > >>> Consider modifying your ~/.grace/templates/Default.agr file to
> specify
> > >>> Helvetica as "font 0" (the default) and change 'xaxis label char
> size'
> > >> to 1.25
> > >>> (from 1.0); same for yaxis.
> > >>>
> > >>> 2. A single .agr file has both the data and the formatting in a
> single
> > >> file.
> > >>> This is good if you come back months or years later and don't
> remember
> > >> your
> > >>> file naming conventions.
> > >>>
> > >>> 3. You can also write simple scripts to systematically modify lots of
> > >>> files, to replace the data but keep the formatting, etc. Once you
> grok
> > >> the
> > >>> file syntax (which is pretty straightforward), it's about as easy to
> > >> write
> > >>> scripts to create or manipulate xmgrace files as it is to write
> gnuplot
> > >> or
> > >>> matplotlib scripts.
> > >>>
> > >>> 4. Consider aliasing xmgrace to 'xmgrace -hdevice PDF'. This means
> > that
> > >>> "print" will create a PDF file (rather than the default PostScript).
> > >> This is
> > >>> likely to be what most people want.
> > >>>
> > >>> ....dac
> > >>>
> > >>> (OK: I realize I've probably started a flame war here... Next up: why
> > you
> > >>> should write all your code in LISP.)
> > >>>
> > >>> _______________________________________________
> > >>> 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
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 16
> Date: Mon, 1 Feb 2016 15:52:42 +0100
> From: Jean-Patrick Francoia <jeanpatrick.francoia.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: amber.ambermd.org
> Message-ID: <56AF713A.7000903.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Here you are
>
> Le 01/02/2016 15:36, Jason Swails a ?crit :
> > Can you provide the mdout file that failed here?
> >
> > On Mon, Feb 1, 2016 at 9:32 AM, Jean-Patrick Francoia <
> > jeanpatrick.francoia.gmail.com> wrote:
> >
> >> Cool.
> >>
> >> It's buggy however:
> >>
> >> Traceback (most recent call last):
> >> File "/home/djipey/SOFT/amber14/bin/mdout_analyzer.py", line 63, in
> >> <module>
> >> mdout = MdoutClass(f)
> >> File
> >>
> >>
> "/home/djipey/SOFT/amber14/lib/python2.7/site-packages/mdoutanalyzer/mdout.py",
> >> line 82, in __init__
> >> if self.properties['imin'] == 5:
> >> KeyError: 'imin'
> >>
> >> Le 01/02/2016 15:05, Jason Swails a ?crit :
> >>> If you're trying to plot data from mdout files, you can always try
> >>> "mdout_analyzer.py". It's built on top of matplotlib and doesn't
> require
> >>> any pre-processing step for mdout files (i.e., you can just type:
> >>>
> >>> mdout_analyzer.py mdout1 mdout2 ... mdoutN
> >>> )
> >>>
> >>> HTH,
> >>> Jason
> >>>
> >>> On Mon, Feb 1, 2016 at 8:57 AM, Jean-Patrick Francoia <
> >>> jeanpatrick.francoia.gmail.com> wrote:
> >>>
> >>>> "Plots generally look good"...Yeah maybe with a little formatting as
> you
> >>>> suggested. Actually xmgrace has an old look on my platform, a bit like
> >>>> xleap. That's why I will go for gnuplot.
> >>>>
> >>>> I had a bit of spare time, so I wrote a quick script:
> >>>>
> >>>> #!/usr/bin/python
> >>>> # coding: utf-8
> >>>>
> >>>> help = """Plot.py
> >>>>
> >>>> Script to plot (x, y) data from files
> >>>>
> >>>> Usage:
> >>>> plot.py <files>...
> >>>>
> >>>> Options:
> >>>> -h --help Display help
> >>>> """
> >>>>
> >>>>
> >>>> from docopt import docopt
> >>>> import matplotlib.pyplot as plt
> >>>>
> >>>> plt.style.use('ggplot')
> >>>> plt.style.use('seaborn-poster')
> >>>> plt.tick_params(left='off', bottom='off', top='off', right='off')
> >>>>
> >>>>
> >>>> arguments = docopt(help)
> >>>>
> >>>> for arg in arguments['<files>']:
> >>>> pts_x = []
> >>>> pts_y = []
> >>>>
> >>>> with open(arg, 'r') as f:
> >>>> for line in f.readlines():
> >>>> res = [float(value.strip()) for value in line.split('
> ')
> >>>> if value.strip() != '']
> >>>> if res:
> >>>> pts_x.append(res[0])
> >>>> pts_y.append(res[1])
> >>>>
> >>>> plt.plot(pts_x, pts_y, label=arg)
> >>>>
> >>>> plt.legend()
> >>>> plt.show()
> >>>>
> >>>> Just to try docopt and the new version of matplotlib (which includes
> >>>> styles). The graph formatting is clearly R-inspired (the devs of
> >>>> matplotlib finally underestood...).
> >>>>
> >>>> Usage:
> >>>> ./plot.py summary.EPTOT summary.ETOT
> >>>>
> >>>> Result:
> >>>> http://i.imgur.com/FPdBfsz.png
> >>>>
> >>>> Le 01/02/2016 14:08, David A Case a ?crit :
> >>>>> On Mon, Feb 01, 2016, Lorenzo Gontrani wrote:
> >>>>>
> >>>>>> xmgrace is great..and lightweight.
> >>>>> Just some (off-topic) comments about why I like xmgrace:
> >>>>>
> >>>>> 1. Plots generally look good and can be interactively edited if they
> >>>> don't.
> >>>>> Consider modifying your ~/.grace/templates/Default.agr file to
> specify
> >>>>> Helvetica as "font 0" (the default) and change 'xaxis label char
> size'
> >>>> to 1.25
> >>>>> (from 1.0); same for yaxis.
> >>>>>
> >>>>> 2. A single .agr file has both the data and the formatting in a
> single
> >>>> file.
> >>>>> This is good if you come back months or years later and don't
> remember
> >>>> your
> >>>>> file naming conventions.
> >>>>>
> >>>>> 3. You can also write simple scripts to systematically modify lots of
> >>>>> files, to replace the data but keep the formatting, etc. Once you
> grok
> >>>> the
> >>>>> file syntax (which is pretty straightforward), it's about as easy to
> >>>> write
> >>>>> scripts to create or manipulate xmgrace files as it is to write
> gnuplot
> >>>> or
> >>>>> matplotlib scripts.
> >>>>>
> >>>>> 4. Consider aliasing xmgrace to 'xmgrace -hdevice PDF'. This means
> >> that
> >>>>> "print" will create a PDF file (rather than the default PostScript).
> >>>> This is
> >>>>> likely to be what most people want.
> >>>>>
> >>>>> ....dac
> >>>>>
> >>>>> (OK: I realize I've probably started a flame war here... Next up: why
> >> you
> >>>>> should write all your code in LISP.)
> >>>>>
> >>>>> _______________________________________________
> >>>>> 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
> >>
> >
> >
>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: mdout.py
> Type: text/x-python
> Size: 16789 bytes
> Desc: not available
> Url :
> http://lists.ambermd.org/mailman/private/amber/attachments/20160201/01fbb08e/attachment-0001.py
>
> ------------------------------
>
> Message: 17
> Date: Mon, 1 Feb 2016 11:27:51 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAEk9e3qRCy9fG3L1L1xca3r9c3pr_aQv_DzP2NbSey2hSwoNTw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Feb 1, 2016 at 9:52 AM, Jean-Patrick Francoia <
> jeanpatrick.francoia.gmail.com> wrote:
>
> > Here you are
>
>
> ?That's the mdout.py source code, I meant the mdout file that is failing to
> get parsed by mdout.py.
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 18
> Date: Mon, 1 Feb 2016 12:09:55 -0500
> From: Hai Nguyen <nhai.qn.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAFNMPM8PsEpwe3XNR4N5D7953sbmqs4svRHS4JsOrZrQ_fPhsA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> to make beautiful plot with little effort, I would give seaborn a shot
> http://stanford.edu/~mwaskom/software/seaborn/examples/index.html
>
> (pip install matplotlib seaborn)
>
> Note: new version of matplotlib use seaborn style but there still requires
> much effort to have nice plot.
>
> Hai
>
> On Mon, Feb 1, 2016 at 8:57 AM, Jean-Patrick Francoia <
> jeanpatrick.francoia.gmail.com> wrote:
>
> > "Plots generally look good"...Yeah maybe with a little formatting as you
> > suggested. Actually xmgrace has an old look on my platform, a bit like
> > xleap. That's why I will go for gnuplot.
> >
> > I had a bit of spare time, so I wrote a quick script:
> >
> > #!/usr/bin/python
> > # coding: utf-8
> >
> > help = """Plot.py
> >
> > Script to plot (x, y) data from files
> >
> > Usage:
> > plot.py <files>...
> >
> > Options:
> > -h --help Display help
> > """
> >
> >
> > from docopt import docopt
> > import matplotlib.pyplot as plt
> >
> > plt.style.use('ggplot')
> > plt.style.use('seaborn-poster')
> > plt.tick_params(left='off', bottom='off', top='off', right='off')
> >
> >
> > arguments = docopt(help)
> >
> > for arg in arguments['<files>']:
> > pts_x = []
> > pts_y = []
> >
> > with open(arg, 'r') as f:
> > for line in f.readlines():
> > res = [float(value.strip()) for value in line.split(' ')
> > if value.strip() != '']
> > if res:
> > pts_x.append(res[0])
> > pts_y.append(res[1])
> >
> > plt.plot(pts_x, pts_y, label=arg)
> >
> > plt.legend()
> > plt.show()
> >
> > Just to try docopt and the new version of matplotlib (which includes
> > styles). The graph formatting is clearly R-inspired (the devs of
> > matplotlib finally underestood...).
> >
> > Usage:
> > ./plot.py summary.EPTOT summary.ETOT
> >
> > Result:
> > http://i.imgur.com/FPdBfsz.png
> >
> > Le 01/02/2016 14:08, David A Case a ?crit :
> > > On Mon, Feb 01, 2016, Lorenzo Gontrani wrote:
> > >
> > >> xmgrace is great..and lightweight.
> > > Just some (off-topic) comments about why I like xmgrace:
> > >
> > > 1. Plots generally look good and can be interactively edited if they
> > don't.
> > > Consider modifying your ~/.grace/templates/Default.agr file to specify
> > > Helvetica as "font 0" (the default) and change 'xaxis label char size'
> > to 1.25
> > > (from 1.0); same for yaxis.
> > >
> > > 2. A single .agr file has both the data and the formatting in a single
> > file.
> > > This is good if you come back months or years later and don't remember
> > your
> > > file naming conventions.
> > >
> > > 3. You can also write simple scripts to systematically modify lots of
> > > files, to replace the data but keep the formatting, etc. Once you grok
> > the
> > > file syntax (which is pretty straightforward), it's about as easy to
> > write
> > > scripts to create or manipulate xmgrace files as it is to write gnuplot
> > or
> > > matplotlib scripts.
> > >
> > > 4. Consider aliasing xmgrace to 'xmgrace -hdevice PDF'. This means
> that
> > > "print" will create a PDF file (rather than the default PostScript).
> > This is
> > > likely to be what most people want.
> > >
> > > ....dac
> > >
> > > (OK: I realize I've probably started a flame war here... Next up: why
> you
> > > should write all your code in LISP.)
> > >
> > > _______________________________________________
> > > 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
> >
>
>
> ------------------------------
>
> Message: 19
> Date: Mon, 1 Feb 2016 20:27:13 +0100
> From: Jean-Patrick Francoia <jeanpatrick.francoia.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: amber.ambermd.org
> Message-ID: <56AFB191.8080702.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Sorry, I misunderstood. Here you are (again).
>
> Le 01/02/2016 15:52, Jean-Patrick Francoia a ?crit :
> > Here you are
> >
> > Le 01/02/2016 15:36, Jason Swails a ?crit :
> >> Can you provide the mdout file that failed here?
> >>
> >> On Mon, Feb 1, 2016 at 9:32 AM, Jean-Patrick Francoia <
> >> jeanpatrick.francoia.gmail.com> wrote:
> >>
> >>> Cool.
> >>>
> >>> It's buggy however:
> >>>
> >>> Traceback (most recent call last):
> >>> File "/home/djipey/SOFT/amber14/bin/mdout_analyzer.py", line 63, in
> >>> <module>
> >>> mdout = MdoutClass(f)
> >>> File
> >>>
> >>>
> "/home/djipey/SOFT/amber14/lib/python2.7/site-packages/mdoutanalyzer/mdout.py",
> >>>
> >>> line 82, in __init__
> >>> if self.properties['imin'] == 5:
> >>> KeyError: 'imin'
> >>>
> >>> Le 01/02/2016 15:05, Jason Swails a ?crit :
> >>>> If you're trying to plot data from mdout files, you can always try
> >>>> "mdout_analyzer.py". It's built on top of matplotlib and doesn't
> >>>> require
> >>>> any pre-processing step for mdout files (i.e., you can just type:
> >>>>
> >>>> mdout_analyzer.py mdout1 mdout2 ... mdoutN
> >>>> )
> >>>>
> >>>> HTH,
> >>>> Jason
> >>>>
> >>>> On Mon, Feb 1, 2016 at 8:57 AM, Jean-Patrick Francoia <
> >>>> jeanpatrick.francoia.gmail.com> wrote:
> >>>>
> >>>>> "Plots generally look good"...Yeah maybe with a little formatting
> >>>>> as you
> >>>>> suggested. Actually xmgrace has an old look on my platform, a bit
> >>>>> like
> >>>>> xleap. That's why I will go for gnuplot.
> >>>>>
> >>>>> I had a bit of spare time, so I wrote a quick script:
> >>>>>
> >>>>> #!/usr/bin/python
> >>>>> # coding: utf-8
> >>>>>
> >>>>> help = """Plot.py
> >>>>>
> >>>>> Script to plot (x, y) data from files
> >>>>>
> >>>>> Usage:
> >>>>> plot.py <files>...
> >>>>>
> >>>>> Options:
> >>>>> -h --help Display help
> >>>>> """
> >>>>>
> >>>>>
> >>>>> from docopt import docopt
> >>>>> import matplotlib.pyplot as plt
> >>>>>
> >>>>> plt.style.use('ggplot')
> >>>>> plt.style.use('seaborn-poster')
> >>>>> plt.tick_params(left='off', bottom='off', top='off', right='off')
> >>>>>
> >>>>>
> >>>>> arguments = docopt(help)
> >>>>>
> >>>>> for arg in arguments['<files>']:
> >>>>> pts_x = []
> >>>>> pts_y = []
> >>>>>
> >>>>> with open(arg, 'r') as f:
> >>>>> for line in f.readlines():
> >>>>> res = [float(value.strip()) for value in
> >>>>> line.split(' ')
> >>>>> if value.strip() != '']
> >>>>> if res:
> >>>>> pts_x.append(res[0])
> >>>>> pts_y.append(res[1])
> >>>>>
> >>>>> plt.plot(pts_x, pts_y, label=arg)
> >>>>>
> >>>>> plt.legend()
> >>>>> plt.show()
> >>>>>
> >>>>> Just to try docopt and the new version of matplotlib (which includes
> >>>>> styles). The graph formatting is clearly R-inspired (the devs of
> >>>>> matplotlib finally underestood...).
> >>>>>
> >>>>> Usage:
> >>>>> ./plot.py summary.EPTOT summary.ETOT
> >>>>>
> >>>>> Result:
> >>>>> http://i.imgur.com/FPdBfsz.png
> >>>>>
> >>>>> Le 01/02/2016 14:08, David A Case a ?crit :
> >>>>>> On Mon, Feb 01, 2016, Lorenzo Gontrani wrote:
> >>>>>>
> >>>>>>> xmgrace is great..and lightweight.
> >>>>>> Just some (off-topic) comments about why I like xmgrace:
> >>>>>>
> >>>>>> 1. Plots generally look good and can be interactively edited if they
> >>>>> don't.
> >>>>>> Consider modifying your ~/.grace/templates/Default.agr file to
> >>>>>> specify
> >>>>>> Helvetica as "font 0" (the default) and change 'xaxis label char
> >>>>>> size'
> >>>>> to 1.25
> >>>>>> (from 1.0); same for yaxis.
> >>>>>>
> >>>>>> 2. A single .agr file has both the data and the formatting in a
> >>>>>> single
> >>>>> file.
> >>>>>> This is good if you come back months or years later and don't
> >>>>>> remember
> >>>>> your
> >>>>>> file naming conventions.
> >>>>>>
> >>>>>> 3. You can also write simple scripts to systematically modify
> >>>>>> lots of
> >>>>>> files, to replace the data but keep the formatting, etc. Once
> >>>>>> you grok
> >>>>> the
> >>>>>> file syntax (which is pretty straightforward), it's about as easy to
> >>>>> write
> >>>>>> scripts to create or manipulate xmgrace files as it is to write
> >>>>>> gnuplot
> >>>>> or
> >>>>>> matplotlib scripts.
> >>>>>>
> >>>>>> 4. Consider aliasing xmgrace to 'xmgrace -hdevice PDF'. This means
> >>> that
> >>>>>> "print" will create a PDF file (rather than the default PostScript).
> >>>>> This is
> >>>>>> likely to be what most people want.
> >>>>>>
> >>>>>> ....dac
> >>>>>>
> >>>>>> (OK: I realize I've probably started a flame war here... Next up:
> >>>>>> why
> >>> you
> >>>>>> should write all your code in LISP.)
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> 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
> >>>
> >>
> >>
> >
>
> -------------- next part --------------
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> 98.600 726.8861
> 98.800 701.5287
> 99.000 729.1545
> 99.200 739.6670
> 99.400 760.2253
> 99.600 744.5564
> 99.800 734.4232
> 100.000 759.7508
> 100.200 764.8375
> 100.400 776.9930
> 100.600 747.1309
> 100.800 765.4914
> 101.000 775.4631
> 101.200 782.9019
> 101.400 779.2129
> 101.600 775.8828
> 101.800 776.1350
> 102.000 790.0787
> 102.200 784.7263
> 102.400 746.5736
> 102.600 806.8400
> 102.800 790.1193
> 103.000 795.1792
> 103.200 771.1887
> 103.400 779.9466
> 103.600 738.3369
> 103.800 780.6264
> 104.000 735.7744
> 104.200 768.3410
> 104.400 770.6998
> 104.600 755.2913
> 104.800 779.7275
> 105.000 784.6206
> 105.200 758.7277
> 105.400 778.5122
> 105.600 787.9274
> 105.800 754.5440
> 106.000 763.4598
> 106.200 744.5990
> 106.400 759.9856
> 106.600 759.3398
> 106.800 751.5678
> 107.000 733.5137
> 107.200 741.7776
> 107.400 764.0266
> 107.600 737.7444
> 107.800 739.9722
> 108.000 789.0040
> 108.200 752.2174
> 108.400 762.1101
> 108.600 760.9671
> 108.800 766.5675
> 109.000 781.6284
> 109.200 747.0240
> 109.400 755.2484
> 109.600 769.9789
> 109.800 827.3733
> 110.000 741.5189
> 110.200 784.8143
> 110.400 778.6374
> 110.600 766.9330
> 110.800 750.3049
> 111.000 763.6017
> 111.200 768.7993
> 111.400 764.7324
> 111.600 750.3411
> 111.800 785.5239
> 112.000 773.2335
> 112.200 772.9315
> 112.400 727.2342
> 112.600 753.0187
> 112.800 763.9356
> 113.000 742.4686
> 113.200 795.5822
> 113.400 780.0323
> 113.600 783.8092
> 113.800 761.3986
> 114.000 773.8407
> 114.200 776.4837
> 114.400 803.9624
> 114.600 787.8491
> 114.800 766.4455
> 115.000 770.9259
> 115.200 776.8104
> 115.400 745.1387
> 115.600 751.8670
> 115.800 776.0270
> 116.000 749.3704
> 116.200 772.3998
> 116.400 800.3853
> 116.600 774.5230
> 116.800 765.2082
> 117.000 766.3880
> 117.200 755.5992
> 117.400 801.5156
> 117.600 769.5502
> 117.800 752.7901
> 118.000 739.9830
> 118.200 736.9519
> 118.400 746.2697
> 118.600 761.5246
> 118.800 730.3087
> 119.000 781.7931
> 119.200 737.2280
> 119.400 756.1793
> 119.600 741.2579
> 119.800 741.2213
> 120.000 735.6930
> 120.200 714.0749
> 120.400 773.4635
> 120.600 754.2670
> 120.800 733.4160
> 121.000 781.5249
> 121.200 725.8586
> 121.400 754.8089
> 121.600 764.7110
> 121.800 771.3689
> 122.000 766.4627
> 122.200 755.6994
> 122.400 791.0588
> 122.600 745.7757
> 122.800 761.2515
> 123.000 806.6574
> 123.200 800.6803
> 123.400 781.6740
> 123.600 786.0030
> 123.800 766.4136
> 124.000 782.1865
> 124.200 773.1100
> 124.400 772.7421
> 124.600 770.6152
> 124.800 793.2147
> 125.000 743.5486
> 125.200 761.5868
> 125.400 776.0001
> 125.600 811.1618
> 125.800 767.3427
> 126.000 756.8936
> 126.200 763.4053
> 126.400 755.3924
> 126.600 772.2755
> 126.800 768.6817
> 127.000 757.4310
> 127.200 728.1142
> 127.400 734.4446
> 127.600 704.6929
> 127.800 717.8825
> 128.000 743.6934
> 128.200 738.6153
> 128.400 760.7505
> 128.600 744.3316
> 128.800 699.8004
> 129.000 785.5094
> 129.200 775.8862
> 129.400 762.3329
> 129.600 787.0396
> 129.800 741.2914
> 130.000 763.4190
> 130.200 752.7559
> 130.400 740.2151
> 130.600 728.6025
> 130.800 715.3943
> 131.000 730.7973
> 131.200 739.1482
> 131.400 757.4432
> 131.600 717.4386
> 131.800 748.9057
> 132.000 744.8122
> 132.200 763.9836
> 132.400 761.6329
> 132.600 759.3430
> 132.800 789.2265
> 133.000 768.1631
> 133.200 760.5390
> 133.400 733.7618
> 133.600 758.9357
> 133.800 783.1848
> 134.000 756.2475
> 134.200 761.2312
> 134.400 741.8990
> 134.600 757.8818
> 134.800 762.1238
> 135.000 744.6653
> 135.200 776.9482
> 135.400 777.7447
> 135.600 776.3010
> 135.800 792.5011
> 136.000 781.4024
> 136.200 766.4976
> 136.400 777.2410
> 136.600 764.8168
> 136.800 772.7926
> 137.000 759.3226
> 137.200 779.2675
> 137.400 773.8494
> 137.600 755.9152
> 137.800 750.7961
> 138.000 761.1662
> 138.200 764.0161
> 138.400 737.3401
> 138.600 757.5740
> 138.800 749.7337
> 139.000 753.9213
> 139.200 752.5092
> 139.400 713.4706
> 139.600 746.7098
> 139.800 756.1835
> 140.000 744.1924
> 140.200 739.5159
> 140.400 755.0017
> 140.600 735.9693
> 140.800 721.1449
> 141.000 734.5747
> 141.200 763.0857
> 141.400 751.9037
> 141.600 710.0687
> 141.800 734.3802
> 142.000 762.3141
> 142.200 740.8404
> 142.400 738.8941
> 142.600 740.0569
> 142.800 765.0540
> 143.000 743.2016
> 143.200 750.9804
> 143.400 761.3245
> 143.600 780.9562
> 143.800 791.6769
> 144.000 798.4784
> 144.200 757.7939
> 144.400 793.8237
> 144.600 758.4038
> 144.800 789.5482
> 145.000 750.4850
> 145.200 773.9908
> 145.400 775.5261
> 145.600 762.6859
> 145.800 778.5874
> 146.000 755.2517
> 146.200 772.1846
> 146.400 751.0324
> 146.600 730.3753
> 146.800 732.3388
> 147.000 748.1909
> 147.200 741.0005
> 147.400 760.1704
> 147.600 755.3464
> 147.800 771.7939
> 148.000 744.6774
> 148.200 735.9292
> 148.400 733.7870
> 148.600 737.7871
> 148.800 755.0910
> 149.000 760.6355
> 149.200 747.5229
> 149.400 713.1765
> 149.600 777.9191
> 149.800 755.2995
> 150.000 736.8578
> 150.200 727.8661
> 150.400 730.8643
> 150.600 771.0934
> 150.800 714.2780
> 151.000 744.4643
> 151.200 711.6738
> 151.400 747.0397
> 151.600 779.4228
> 151.800 783.9103
> 152.000 770.8814
> 152.200 759.9738
> 152.400 754.9698
> 152.600 744.2514
> 152.800 750.6269
> 153.000 758.7260
> 153.200 805.6087
> 153.400 783.5341
> 153.600 787.6778
> 153.800 785.9240
> 154.000 792.6866
> 154.200 773.5874
> 154.400 757.5270
> 154.600 759.5338
> 154.800 755.8650
> 155.000 759.6743
> 155.200 744.1380
> 155.400 796.1283
> 155.600 767.3771
> 155.800 778.9006
> 156.000 770.6592
> 156.200 732.7711
> 156.400 785.1642
> 156.600 730.4089
> 156.800 714.2378
> 157.000 738.5341
> 157.200 749.2357
> 157.400 717.7587
> 157.600 750.3592
> 157.800 772.9539
> 158.000 772.7671
> 158.200 760.9973
> 158.400 761.1728
> 158.600 759.7981
> 158.800 742.5851
> 159.000 754.5789
> 159.200 751.1226
> 159.400 717.9324
> 159.600 758.1475
> 159.800 738.3946
> 160.000 745.3506
> 160.200 738.6078
> 160.400 743.8774
> 160.600 760.1796
> 160.800 729.4399
> 161.000 744.5955
> 161.200 759.4878
> 161.400 747.5736
> 161.600 777.6135
> 161.800 754.0746
> 162.000 767.4476
> 162.200 753.1808
> 162.400 751.0146
> 162.600 754.6483
> 162.800 754.9519
> 163.000 750.0496
> 163.200 753.9919
> 163.400 763.7984
> 163.600 755.0688
> 163.800 749.5574
> 164.000 757.6154
> 164.200 756.0147
> 164.400 694.4192
> 164.600 715.6564
> 164.800 721.9564
> 165.000 725.5953
> 165.200 735.1187
> 165.400 757.9285
> 165.600 730.8968
> 165.800 735.8081
> 166.000 718.5215
> 166.200 727.1583
> 166.400 737.8299
> 166.600 738.5896
> 166.800 700.7752
> 167.000 730.9649
> 167.200 735.6644
> 167.400 765.9351
> 167.600 760.5235
> 167.800 774.6080
> 168.000 749.3988
> 168.200 765.0912
> 168.400 744.9610
> 168.600 782.3931
> 168.800 786.8347
> 169.000 761.3052
> 169.200 734.5957
> 169.400 750.1895
> 169.600 745.9128
> 169.800 760.0173
> 170.000 772.5057
> 170.200 742.4391
> 170.400 753.7216
> 170.600 761.1689
> 170.800 804.0503
> 171.000 786.0748
> 171.200 744.9143
> 171.400 779.6524
> 171.600 782.9636
> 171.800 763.0941
> 172.000 761.3571
> 172.200 784.7536
> 172.400 772.1861
> 172.600 751.2080
> 172.800 785.3610
> 173.000 768.1936
> 173.200 793.5175
> 173.400 777.7432
> 173.600 763.6337
> 173.800 740.1212
> 174.000 799.6339
> 174.200 724.2982
> 174.400 766.4098
> 174.600 829.8716
> 174.800 813.7479
> 175.000 772.8579
> 175.200 765.5082
> 175.400 738.5263
> 175.600 774.7093
> 175.800 775.2624
> 176.000 783.0622
> 176.200 791.5054
> 176.400 777.6397
> 176.600 744.0969
> 176.800 740.2122
> 177.000 771.3829
> 177.200 773.8111
> 177.400 766.6310
> 177.600 792.9981
> 177.800 766.2040
> 178.000 736.1604
> 178.200 744.0776
> 178.400 786.7343
> 178.600 784.8378
> 178.800 779.0456
> 179.000 754.7851
> 179.200 776.7418
> 179.400 758.6776
> 179.600 751.5839
> 179.800 758.0097
> 180.000 743.8758
> 180.200 744.2613
> 180.400 774.6877
> 180.600 725.8468
> 180.800 753.1912
> 181.000 759.6514
> 181.200 758.3429
> 181.400 755.1453
> 181.600 778.5987
> 181.800 751.3523
> 182.000 785.1233
> 182.200 761.1507
> 182.400 768.9753
> 182.600 764.2212
> 182.800 772.2488
> 183.000 765.8680
> 183.200 740.2608
> 183.400 766.4712
> 183.600 787.1808
> 183.800 753.8216
> 184.000 778.0833
> 184.200 752.4945
> 184.400 795.8689
> 184.600 769.7974
> 184.800 782.6309
> 185.000 787.8218
> 185.200 792.9215
> 185.400 794.5090
> 185.600 810.8003
> 185.800 768.7432
> 186.000 730.8004
> 186.200 765.1937
> 186.400 790.7948
> 186.600 781.2069
> 186.800 745.4072
> 187.000 819.6791
> 187.200 775.0331
> 187.400 774.7376
> 187.600 763.1392
> 187.800 780.5710
> 188.000 748.2901
> 188.200 742.3168
> 188.400 745.8254
> 188.600 740.0448
> 188.800 752.4317
> 189.000 755.4287
> 189.200 770.3927
> 189.400 764.7785
> 189.600 792.5664
> 189.800 779.7668
> 190.000 763.2534
> 190.200 762.2078
> 190.400 765.2073
> 190.600 776.3148
> 190.800 743.3964
> 191.000 749.8699
> 191.200 758.7402
> 191.400 745.7598
> 191.600 733.9167
> 191.800 733.2654
> 192.000 739.0634
> 192.200 728.9881
> 192.400 737.6808
> 192.600 760.7403
> 192.800 740.9245
> 193.000 756.8566
> 193.200 743.3764
> 193.400 765.9847
> 193.600 730.0505
> 193.800 788.4712
> 194.000 736.1185
> 194.200 791.8068
> 194.400 754.5443
> 194.600 756.6138
> 194.800 778.1540
> 195.000 788.2224
> 195.200 779.5346
> 195.400 747.5234
> 195.600 753.3427
> 195.800 736.3995
> 196.000 730.4123
> 196.200 746.7954
> 196.400 759.2831
> 196.600 781.8824
> 196.800 807.8572
> 197.000 743.1657
> 197.200 769.7039
> 197.400 766.0189
> 197.600 754.8144
> 197.800 779.3333
> 198.000 772.8604
> 198.200 778.6742
> 198.400 760.3842
> 198.600 779.8045
> 198.800 760.9632
> 199.000 770.6872
> 199.200 784.0654
> 199.400 726.8250
> 199.600 784.0594
> 199.800 746.1834
> 200.000 735.7055
>
> ------------------------------
>
> Message: 20
> Date: Mon, 1 Feb 2016 14:32:26 -0500
> From: Hai Nguyen <nhai.qn.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFNMPM9DB-9eG3dXwBXAh4cgg7AcjnM3HKk7HBK=
> RdDQjSZJYg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> this is not (still) mdout file.
>
> (example:
>
> http://ambermd.org/tutorials/basic/tutorial1/files/output_files/polyAT_vac_md1_12Acut.out
> )
>
> Hai
>
> On Mon, Feb 1, 2016 at 2:27 PM, Jean-Patrick Francoia <
> jeanpatrick.francoia.gmail.com> wrote:
>
> > Sorry, I misunderstood. Here you are (again).
> >
> >
> > Le 01/02/2016 15:52, Jean-Patrick Francoia a ?crit :
> >
> >> Here you are
> >>
> >> Le 01/02/2016 15:36, Jason Swails a ?crit :
> >>
> >>> Can you provide the mdout file that failed here?
> >>>
> >>> On Mon, Feb 1, 2016 at 9:32 AM, Jean-Patrick Francoia <
> >>> jeanpatrick.francoia.gmail.com> wrote:
> >>>
> >>> Cool.
> >>>>
> >>>> It's buggy however:
> >>>>
> >>>> Traceback (most recent call last):
> >>>> File "/home/djipey/SOFT/amber14/bin/mdout_analyzer.py", line 63,
> in
> >>>> <module>
> >>>> mdout = MdoutClass(f)
> >>>> File
> >>>>
> >>>>
> "/home/djipey/SOFT/amber14/lib/python2.7/site-packages/mdoutanalyzer/mdout.py",
> >>>>
> >>>> line 82, in __init__
> >>>> if self.properties['imin'] == 5:
> >>>> KeyError: 'imin'
> >>>>
> >>>> Le 01/02/2016 15:05, Jason Swails a ?crit :
> >>>>
> >>>>> If you're trying to plot data from mdout files, you can always try
> >>>>> "mdout_analyzer.py". It's built on top of matplotlib and doesn't
> >>>>> require
> >>>>> any pre-processing step for mdout files (i.e., you can just type:
> >>>>>
> >>>>> mdout_analyzer.py mdout1 mdout2 ... mdoutN
> >>>>> )
> >>>>>
> >>>>> HTH,
> >>>>> Jason
> >>>>>
> >>>>> On Mon, Feb 1, 2016 at 8:57 AM, Jean-Patrick Francoia <
> >>>>> jeanpatrick.francoia.gmail.com> wrote:
> >>>>>
> >>>>> "Plots generally look good"...Yeah maybe with a little formatting as
> >>>>>> you
> >>>>>> suggested. Actually xmgrace has an old look on my platform, a bit
> like
> >>>>>> xleap. That's why I will go for gnuplot.
> >>>>>>
> >>>>>> I had a bit of spare time, so I wrote a quick script:
> >>>>>>
> >>>>>> #!/usr/bin/python
> >>>>>> # coding: utf-8
> >>>>>>
> >>>>>> help = """Plot.py
> >>>>>>
> >>>>>> Script to plot (x, y) data from files
> >>>>>>
> >>>>>> Usage:
> >>>>>> plot.py <files>...
> >>>>>>
> >>>>>> Options:
> >>>>>> -h --help Display help
> >>>>>> """
> >>>>>>
> >>>>>>
> >>>>>> from docopt import docopt
> >>>>>> import matplotlib.pyplot as plt
> >>>>>>
> >>>>>> plt.style.use('ggplot')
> >>>>>> plt.style.use('seaborn-poster')
> >>>>>> plt.tick_params(left='off', bottom='off', top='off', right='off')
> >>>>>>
> >>>>>>
> >>>>>> arguments = docopt(help)
> >>>>>>
> >>>>>> for arg in arguments['<files>']:
> >>>>>> pts_x = []
> >>>>>> pts_y = []
> >>>>>>
> >>>>>> with open(arg, 'r') as f:
> >>>>>> for line in f.readlines():
> >>>>>> res = [float(value.strip()) for value in line.split('
> >>>>>> ')
> >>>>>> if value.strip() != '']
> >>>>>> if res:
> >>>>>> pts_x.append(res[0])
> >>>>>> pts_y.append(res[1])
> >>>>>>
> >>>>>> plt.plot(pts_x, pts_y, label=arg)
> >>>>>>
> >>>>>> plt.legend()
> >>>>>> plt.show()
> >>>>>>
> >>>>>> Just to try docopt and the new version of matplotlib (which includes
> >>>>>> styles). The graph formatting is clearly R-inspired (the devs of
> >>>>>> matplotlib finally underestood...).
> >>>>>>
> >>>>>> Usage:
> >>>>>> ./plot.py summary.EPTOT summary.ETOT
> >>>>>>
> >>>>>> Result:
> >>>>>> http://i.imgur.com/FPdBfsz.png
> >>>>>>
> >>>>>> Le 01/02/2016 14:08, David A Case a ?crit :
> >>>>>>
> >>>>>>> On Mon, Feb 01, 2016, Lorenzo Gontrani wrote:
> >>>>>>>
> >>>>>>> xmgrace is great..and lightweight.
> >>>>>>>>
> >>>>>>> Just some (off-topic) comments about why I like xmgrace:
> >>>>>>>
> >>>>>>> 1. Plots generally look good and can be interactively edited if
> they
> >>>>>>>
> >>>>>> don't.
> >>>>>>
> >>>>>>> Consider modifying your ~/.grace/templates/Default.agr file to
> >>>>>>> specify
> >>>>>>> Helvetica as "font 0" (the default) and change 'xaxis label char
> >>>>>>> size'
> >>>>>>>
> >>>>>> to 1.25
> >>>>>>
> >>>>>>> (from 1.0); same for yaxis.
> >>>>>>>
> >>>>>>> 2. A single .agr file has both the data and the formatting in a
> >>>>>>> single
> >>>>>>>
> >>>>>> file.
> >>>>>>
> >>>>>>> This is good if you come back months or years later and don't
> >>>>>>> remember
> >>>>>>>
> >>>>>> your
> >>>>>>
> >>>>>>> file naming conventions.
> >>>>>>>
> >>>>>>> 3. You can also write simple scripts to systematically modify lots
> of
> >>>>>>> files, to replace the data but keep the formatting, etc. Once you
> >>>>>>> grok
> >>>>>>>
> >>>>>> the
> >>>>>>
> >>>>>>> file syntax (which is pretty straightforward), it's about as easy
> to
> >>>>>>>
> >>>>>> write
> >>>>>>
> >>>>>>> scripts to create or manipulate xmgrace files as it is to write
> >>>>>>> gnuplot
> >>>>>>>
> >>>>>> or
> >>>>>>
> >>>>>>> matplotlib scripts.
> >>>>>>>
> >>>>>>> 4. Consider aliasing xmgrace to 'xmgrace -hdevice PDF'. This means
> >>>>>>>
> >>>>>> that
> >>>>
> >>>>> "print" will create a PDF file (rather than the default PostScript).
> >>>>>>>
> >>>>>> This is
> >>>>>>
> >>>>>>> likely to be what most people want.
> >>>>>>>
> >>>>>>> ....dac
> >>>>>>>
> >>>>>>> (OK: I realize I've probably started a flame war here... Next up:
> why
> >>>>>>>
> >>>>>> you
> >>>>
> >>>>> should write all your code in LISP.)
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> 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
> >
> >
>
>
> ------------------------------
>
> Message: 21
> Date: Mon, 1 Feb 2016 19:50:21 +0000
> From: "Krantzman, Kristin D" <KrantzmanK.cofc.edu>
> Subject: [AMBER] Value of ntrx=7
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <992A5F61E62A024D8E3580E4C42CD4853A6B3868.COLONIAL.COUGARS.INT>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear AMBER Community,
> When restarting a trajectory, do we need to use ntrx=7 to read the box
> information from the inpcrd file?
> Thank you,
> Kristin D. Krantzman
> Professor, Chemistry
> College of Charleston
>
>
> ------------------------------
>
> Message: 22
> Date: Mon, 1 Feb 2016 14:53:43 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Replacement for xmgrace
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAEk9e3rGScCyGhed2ttSTf7Mbn3EEWe-VPwovJNw2h1c_MsvQg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Feb 1, 2016 at 2:27 PM, Jean-Patrick Francoia <
> jeanpatrick.francoia.gmail.com> wrote:
>
> > Sorry, I misunderstood. Here you are (again).
>
>
> ?Yea, that's the summary file generated by process_mdout.pl. The point of
> mdout_analyzer.py is that it natively reads mdout files. So you don't have
> to generate the summary.ENERGY files in the first place -- just give it raw
> mdout files.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 23
> Date: Mon, 1 Feb 2016 14:55:43 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Value of ntrx=7
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3p25rQMx-gqzrjVFV514QjwyEZaH+ShT17e_Z1X=
> dwhKw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Feb 1, 2016 at 2:50 PM, Krantzman, Kristin D <KrantzmanK.cofc.edu>
> wrote:
>
> > Dear AMBER Community,
> > When restarting a trajectory, do we need to use ntrx=7 to read the box
> > information from the inpcrd file?
> >
>
> ?The variable is ntx. The value "7" is the same as "5", although 5 is the
> only one documented in the Amber manual, IIRC. And this is not for reading
> the box information, it's specifying whether or not velocities are present
> in the inpcrd file. If velocities are present, you should use ntx=5 (or
> 7). If they are not present (e.g., following a minimization), set ntx=1.
> The box information will always be looked for if it's needed (and found if
> it's present).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1473, Issue 1
> **************************************
>
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Received on Mon Feb 01 2016 - 18:00:03 PST
