Re: [AMBER] problem in plotting total energy graphs by perl script

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 28 Mar 2016 07:37:52 -0600

I responded to you 3 days ago (http://archive.ambermd.org/201603/0505.html).
Did you not receive my reply?

On Monday, March 28, 2016, Sehrish Naz Aijaz <sehrish.naz.outlook.com>
wrote:

> Dear all,
>
> Please suggest me I am waiting for some reply I am not getting that error
> regarding readdata what to do next its not taking my output files I
> guess....
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Sehrish Naz Aijaz
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>
> *Sent: *25 March 2016 16:18
> *To: *Bill Ross <javascript:_e(%7B%7D,'cvml','ross.cgl.ucsf.edu');>; AMBER
> Mailing List <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>
> *Subject: *Re: [AMBER] problem in plotting total energy graphs by perl
> script
>
>
> Dear Bill,
> I have tried as you said to try just one output file but again its giving
> the following error as,
> writedata enegy.agr 32a_prod5.out
> Writing sets to enegy.agr, format 'Grace File'
> Warning: '32a_prod5.out' selects no data sets.
> Warning: 32a_prod5.out does not correspond to any data sets.
>
> Warning: File 'enegy.agr' has no sets containing data.
>
> And same error message was shown for the command
> Writedata energy.agr 32a_prod5.out_*
>
> Now what to do next please guide me....
>
> Regards,
> Sehrish
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
> From: Bill Ross<mailto:ross.cgl.ucsf.edu
> <javascript:_e(%7B%7D,'cvml','ross.cgl.ucsf.edu');>>
> Sent: 25 March 2016 10:41
> To: AMBER Mailing List<mailto:amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>>
> Subject: Re: [AMBER] problem in plotting total energy graphs by perl script
>
> And
>
> > writedata energy.agr 32a_prod5.out_*
>
> On 3/24/16 10:39 PM, Bill Ross wrote:
> > Just for fun, please try
> >
> > > writedata
> >
> > and
> >
> > > writedata energy.agr 32a_prod5.out
> >
> > Bill
> >
> > On 3/24/16 9:59 PM, Sehrish Naz Aijaz wrote:
> >> Dear Daniel,
> >> I try to run readdata commands as you mentioned. In the beginning it
> was going well as follows,
> >> CPPTRAJ: Trajectory Analysis. V15.00
> >> ___ ___ ___ ___
> >> | \/ | \/ | \/ |
> >> _|_/\_|_/\_|_/\_|_
> >>
> >> | Date/time: 03/25/16 09:52:32
> >> | Available memory: 550.168 MB
> >>
> >> Loading previous history from log 'cpptraj.log'
> >>> readdata *.out
> >> Reading '32a_prod1.out' as Amber MDOUT file with name
> '32a_prod1.out'
> >> Reading from mdout file: 32a_prod1.out
> >> 4000 frames
> >> Reading '32a_prod2.out' as Amber MDOUT file with name
> '32a_prod2.out'
> >> Reading from mdout file: 32a_prod2.out
> >> 4000 frames
> >> Reading '32a_prod3.out' as Amber MDOUT file with name
> '32a_prod3.out'
> >> Reading from mdout file: 32a_prod3.out
> >> 4000 frames
> >> Reading '32a_prod4.out' as Amber MDOUT file with name
> '32a_prod4.out'
> >> Reading from mdout file: 32a_prod4.out
> >> 4000 frames
> >> Reading '32a_prod5.out' as Amber MDOUT file with name
> '32a_prod5.out'
> >> Reading from mdout file: 32a_prod5.out
> >> 4000 frames
> >>> list dataset
> >> DATASETS:
> >> 75 data sets:
> >> 32a_prod1.out[Etot] "32a_prod1.out_Etot" (double), size is
> 4000
> >> 32a_prod1.out[EPtot] "32a_prod1.out_EPtot" (double), size is
> 4000
> >> 32a_prod1.out[BOND] "32a_prod1.out_BOND" (double), size is
> 4000
> >> 32a_prod1.out[ANGLE] "32a_prod1.out_ANGLE" (double), size is
> 4000
> >> 32a_prod1.out[DIHED] "32a_prod1.out_DIHED" (double), size is
> 4000
> >> 32a_prod1.out[VDW] "32a_prod1.out_VDW" (double), size is 4000
> >> 32a_prod1.out[EELEC] "32a_prod1.out_EELEC" (double), size is
> 4000
> >> 32a_prod1.out[VDW1-4] "32a_prod1.out_VDW1-4" (double), size
> is 4000
> >> 32a_prod1.out[EEL1-4] "32a_prod1.out_EEL1-4" (double), size
> is 4000
> >> 32a_prod1.out[RST] "32a_prod1.out_RST" (double), size is 4000
> >> 32a_prod1.out[Density] "32a_prod1.out_Density" (double), size
> is 4000
> >> 32a_prod1.out[EKtot] "32a_prod1.out_EKtot" (double), size is
> 4000
> >> 32a_prod1.out[VOLUME] "32a_prod1.out_VOLUME" (double), size
> is 4000
> >> 32a_prod1.out[TEMP] "32a_prod1.out_TEMP" (double), size is
> 4000
> >> 32a_prod1.out[PRESS] "32a_prod1.out_PRESS" (double), size is
> 4000
> >> 32a_prod2.out[Etot] "32a_prod2.out_Etot" (double), size is
> 4000
> >> 32a_prod2.out[EPtot] "32a_prod2.out_EPtot" (double), size is
> 4000
> >> 32a_prod2.out[BOND] "32a_prod2.out_BOND" (double), size is
> 4000
> >> 32a_prod2.out[ANGLE] "32a_prod2.out_ANGLE" (double), size is
> 4000
> >> 32a_prod2.out[DIHED] "32a_prod2.out_DIHED" (double), size is
> 4000
> >> 32a_prod2.out[VDW] "32a_prod2.out_VDW" (double), size is 4000
> >> 32a_prod2.out[EELEC] "32a_prod2.out_EELEC" (double), size is
> 4000
> >> 32a_prod2.out[VDW1-4] "32a_prod2.out_VDW1-4" (double), size
> is 4000
> >> 32a_prod2.out[EEL1-4] "32a_prod2.out_EEL1-4" (double), size
> is 4000
> >> 32a_prod2.out[RST] "32a_prod2.out_RST" (double), size is 4000
> >> 32a_prod2.out[Density] "32a_prod2.out_Density" (double), size
> is 4000
> >> 32a_prod2.out[EKtot] "32a_prod2.out_EKtot" (double), size is
> 4000
> >> 32a_prod2.out[VOLUME] "32a_prod2.out_VOLUME" (double), size
> is 4000
> >> 32a_prod2.out[TEMP] "32a_prod2.out_TEMP" (double), size is
> 4000
> >> 32a_prod2.out[PRESS] "32a_prod2.out_PRESS" (double), size is
> 4000
> >> 32a_prod3.out[Etot] "32a_prod3.out_Etot" (double), size is
> 4000
> >> 32a_prod3.out[EPtot] "32a_prod3.out_EPtot" (double), size is
> 4000
> >> 32a_prod3.out[BOND] "32a_prod3.out_BOND" (double), size is
> 4000
> >> 32a_prod3.out[ANGLE] "32a_prod3.out_ANGLE" (double), size is
> 4000
> >> 32a_prod3.out[DIHED] "32a_prod3.out_DIHED" (double), size is
> 4000
> >> 32a_prod3.out[VDW] "32a_prod3.out_VDW" (double), size is 4000
> >> 32a_prod3.out[EELEC] "32a_prod3.out_EELEC" (double), size is
> 4000
> >> 32a_prod3.out[VDW1-4] "32a_prod3.out_VDW1-4" (double), size
> is 4000
> >> 32a_prod3.out[EEL1-4] "32a_prod3.out_EEL1-4" (double), size
> is 4000
> >> 32a_prod3.out[RST] "32a_prod3.out_RST" (double), size is 4000
> >> 32a_prod3.out[Density] "32a_prod3.out_Density" (double), size
> is 4000
> >> 32a_prod3.out[EKtot] "32a_prod3.out_EKtot" (double), size is
> 4000
> >> 32a_prod3.out[VOLUME] "32a_prod3.out_VOLUME" (double), size
> is 4000
> >> 32a_prod3.out[TEMP] "32a_prod3.out_TEMP" (double), size is
> 4000
> >> 32a_prod3.out[PRESS] "32a_prod3.out_PRESS" (double), size is
> 4000
> >> 32a_prod4.out[Etot] "32a_prod4.out_Etot" (double), size is
> 4000
> >> 32a_prod4.out[EPtot] "32a_prod4.out_EPtot" (double), size is
> 4000
> >> 32a_prod4.out[BOND] "32a_prod4.out_BOND" (double), size is
> 4000
> >> 32a_prod4.out[ANGLE] "32a_prod4.out_ANGLE" (double), size is
> 4000
> >> 32a_prod4.out[DIHED] "32a_prod4.out_DIHED" (double), size is
> 4000
> >> 32a_prod4.out[VDW] "32a_prod4.out_VDW" (double), size is 4000
> >> 32a_prod4.out[EELEC] "32a_prod4.out_EELEC" (double), size is
> 4000
> >> 32a_prod4.out[VDW1-4] "32a_prod4.out_VDW1-4" (double), size
> is 4000
> >> 32a_prod4.out[EEL1-4] "32a_prod4.out_EEL1-4" (double), size
> is 4000
> >> 32a_prod4.out[RST] "32a_prod4.out_RST" (double), size is 4000
> >> 32a_prod4.out[Density] "32a_prod4.out_Density" (double), size
> is 4000
> >> 32a_prod4.out[EKtot] "32a_prod4.out_EKtot" (double), size is
> 4000
> >> 32a_prod4.out[VOLUME] "32a_prod4.out_VOLUME" (double), size
> is 4000
> >> 32a_prod4.out[TEMP] "32a_prod4.out_TEMP" (double), size is
> 4000
> >> 32a_prod4.out[PRESS] "32a_prod4.out_PRESS" (double), size is
> 4000
> >> 32a_prod5.out[Etot] "32a_prod5.out_Etot" (double), size is
> 4000
> >> 32a_prod5.out[EPtot] "32a_prod5.out_EPtot" (double), size is
> 4000
> >> 32a_prod5.out[BOND] "32a_prod5.out_BOND" (double), size is
> 4000
> >> 32a_prod5.out[ANGLE] "32a_prod5.out_ANGLE" (double), size is
> 4000
> >> 32a_prod5.out[DIHED] "32a_prod5.out_DIHED" (double), size is
> 4000
> >> 32a_prod5.out[VDW] "32a_prod5.out_VDW" (double), size is 4000
> >> 32a_prod5.out[EELEC] "32a_prod5.out_EELEC" (double), size is
> 4000
> >> 32a_prod5.out[VDW1-4] "32a_prod5.out_VDW1-4" (double), size
> is 4000
> >> 32a_prod5.out[EEL1-4] "32a_prod5.out_EEL1-4" (double), size
> is 4000
> >> 32a_prod5.out[RST] "32a_prod5.out_RST" (double), size is 4000
> >> 32a_prod5.out[Density] "32a_prod5.out_Density" (double), size
> is 4000
> >> 32a_prod5.out[EKtot] "32a_prod5.out_EKtot" (double), size is
> 4000
> >> 32a_prod5.out[VOLUME] "32a_prod5.out_VOLUME" (double), size
> is 4000
> >> 32a_prod5.out[TEMP] "32a_prod5.out_TEMP" (double), size is
> 4000
> >> 32a_prod5.out[PRESS] "32a_prod5.out_PRESS" (double), size is
> 4000
> >> but when I type the command;
> >> writedata energy.agr *.out
> >> it gave the following error;
> >> writedata energy.agr *.out
> >> Writing sets to energy.agr, format 'Grace File'
> >> Warning: '*.out' selects no data sets.
> >> Warning: *.out does not correspond to any data sets.
> >>
> >> Warning: File 'energy.agr' has no sets containing data.
> >> where I am doing mistake???
> >> I try to give all output files in writedata commamd as,
> >>> writedata energy.agr 32a_prod1.out 32a_prod2.out 32a_prod3.out
> 32a_prod4.out 32a_prod5.out
> >> Writing sets to energy.agr, format 'Grace File'
> >> Warning: '32a_prod1.out' selects no data sets.
> >> Warning: 32a_prod1.out does not correspond to any data sets.
> >> Warning: '32a_prod2.out' selects no data sets.
> >> Warning: 32a_prod2.out does not correspond to any data sets.
> >> Warning: '32a_prod3.out' selects no data sets.
> >> Warning: 32a_prod3.out does not correspond to any data sets.
> >> Warning: '32a_prod4.out' selects no data sets.
> >> Warning: 32a_prod4.out does not correspond to any data sets.
> >> Warning: '32a_prod5.out' selects no data sets.
> >> Warning: 32a_prod5.out does not correspond to any data sets.
> >>
> >> Warning: File 'energy.agr' has no sets containing data.
> >> again getting the same error. Please suggest me where am I doing
> mistake??
> >>
> >>
> >> Regards,
> >> Sehrish Naz
> >>
> >>
> >>
> >> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
> >>
> >> From: Daniel Roe<mailto:daniel.r.roe.gmail.com
> <javascript:_e(%7B%7D,'cvml','daniel.r.roe.gmail.com');>>
> >> Sent: 22 March 2016 21:01
> >> Cc: AMBER Mailing List<mailto:amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>>
> >> Subject: Re: [AMBER] problem in plotting total energy graphs by perl
> script
> >>
> >> On Tue, Mar 22, 2016 at 9:50 AM, Sehrish Naz Aijaz
> >> <sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>> wrote:
> >>> Can you please tell me the command you are suggesting because I have
> heard
> >>> this command first time please guide me.
> >> Assuming you have cpptraj installed you can do it interactively. Here
> >> is an example.
> >>
> >> $ cpptraj
> >> > readdata md.out
> >> Reading 'md.out' as Amber MDOUT file with name 'md.out'
> >> Reading from mdout file: md.out
> >> 100000 frames
> >> > list dataset
> >>
> >> DATASETS (14 total):
> >> md.out[Etot] "md.out_Etot" (double), size is 100000
> >> md.out[EPtot] "md.out_EPtot" (double), size is 100000
> >> md.out[BOND] "md.out_BOND" (double), size is 100000
> >> md.out[ANGLE] "md.out_ANGLE" (double), size is 100000
> >> md.out[DIHED] "md.out_DIHED" (double), size is 100000
> >> md.out[VDW] "md.out_VDW" (double), size is 100000
> >> md.out[EELEC] "md.out_EELEC" (double), size is 100000
> >> md.out[VDW1-4] "md.out_VDW1-4" (double), size is 100000
> >> md.out[EEL1-4] "md.out_EEL1-4" (double), size is 100000
> >> md.out[RST] "md.out_RST" (double), size is 100000
> >> md.out[EAMBER] "md.out_EAMBER" (double), size is 100000
> >> md.out[EKtot] "md.out_EKtot" (double), size is 100000
> >> md.out[TEMP] "md.out_TEMP" (double), size is 100000
> >> md.out[PRESS] "md.out_PRESS" (double), size is 100000
> >> > writedata energy.agr md.out[*]
> >> Writing sets to energy.agr, format 'Grace File'
> >> md.out_Etot md.out_EPtot md.out_BOND md.out_ANGLE md.out_DIHED
> >> md.out_VDW md.out_EELEC md.out_VDW1-4 md.out_EEL1-4 md.out_RST
> >> md.out_EAMBER md.out_EKtot md.out_TEMP md.out_PRESS
> >> > quit
> >>
> >> Then the file energy.agr will contain all of your energy data sets. If
> >> you just wanted e.g. the total potential energy you would use
> >> 'writedata eptot.agr md.out[EPtot]' instead.
> >>
> >> Hope this helps.
> >>
> >> -Dan
> >>
> >>> Thanks,
> >>>
> >>>
> >>>
> >>> Sent from Mail for Windows 10
> >>>
> >>>
> >>>
> >>> From: Daniel Roe
> >>> Sent: 21 March 2016 19:38
> >>> To: AMBER Mailing List
> >>>
> >>>
> >>> Subject: Re: [AMBER] problem in plotting total energy graphs by perl
> script
> >>>
> >>>
> >>>
> >>> Hi,
> >>>
> >>> FYI you can also use cpptraj to extract energies from MDOUT files via
> >>> the 'readdata' command. You can then analyze the data or write it out
> >>> into any format supported by cpptraj.
> >>>
> >>> -Dan
> >>>
> >>>
> >>> On Sun, Mar 20, 2016 at 10:56 PM, Sehrish Naz Aijaz
> >>> <sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>> wrote:
> >>>> Dear Bill,
> >>>> Are you asking about mden content in my output files??? Or you are
> saying
> >>>> to use mden file generated during production runs???
> >>>> Can you tell me how can I plot those mden file which scripts will
> help for
> >>>> plotting and processing mden files???
> >>>>
> >>>> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows
> >>>> 10
> >>>>
> >>>> From: Bill Ross<mailto:ross.cgl.ucsf.edu
> <javascript:_e(%7B%7D,'cvml','ross.cgl.ucsf.edu');>>
> >>>> Sent: 20 March 2016 01:11
> >>>> To: AMBER Mailing List<mailto:amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>>
> >>>> Subject: Re: [AMBER] problem in plotting total energy graphs by perl
> >>>> script
> >>>>
> >>>> Have you looked at mden file contents? They could be easier to work
> with.
> >>>>
> >>>> Bill
> >>>>
> >>>> On 3/19/16 3:16 AM, Sehrish Naz Aijaz wrote:
> >>>>> Dear Hai,
> >>>>> I try to run this in my amber12 but it gives the following error.
> Can you
> >>>>> explain this to me...
> >>>>> Traceback (most recent call last):
> >>>>> File "/usr/local/amber14/bin/mdout_analyzer.py", line 3, in
> <module>
> >>>>> from tkFileDialog import askopenfilenames
> >>>>> ImportError: No module named tkFileDialog
> >>>>>
> >>>>> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> >>>>> Windows 10
> >>>>>
> >>>>> From: Hai Nguyen<mailto:nhai.qn.gmail.com
> <javascript:_e(%7B%7D,'cvml','nhai.qn.gmail.com');>>
> >>>>> Sent: 19 March 2016 14:48
> >>>>> To: AMBER Mailing List<mailto:amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>>
> >>>>> Subject: Re: [AMBER] problem in plotting total energy graphs by perl
> >>>>> script
> >>>>>
> >>>>> I think it should be compatible (Jason might correct me if I am
> wrong).
> >>>>>
> >>>>> Here is the tutorial:
> http://jswails.wikidot.com/helpful-scripts#toc8
> >>>>>
> >>>>> Cheers
> >>>>> Hai
> >>>>>
> >>>>> On Sat, Mar 19, 2016 at 2:26 AM, Sehrish Naz Aijaz
> >>>>> <sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>>
> >>>>> wrote:
> >>>>>
> >>>>>> Dear Hai,
> >>>>>> I have amber12 in my system. Is this script compatible for amber12
> which
> >>>>>> I
> >>>>>> think not compatible with amber12. So what should I do???
> >>>>>>
> >>>>>> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> >>>>>> Windows 10
> >>>>>>
> >>>>>> From: Hai Nguyen<mailto:nhai.qn.gmail.com
> <javascript:_e(%7B%7D,'cvml','nhai.qn.gmail.com');>>
> >>>>>> Sent: 19 March 2016 13:56
> >>>>>> To: AMBER Mailing List<mailto:amber.ambermd.org
> <javascript:_e(%7B%7D,'cvml','amber.ambermd.org');>>
> >>>>>> Subject: Re: [AMBER] problem in plotting total energy graphs by perl
> >>>>>> script
> >>>>>>
> >>>>>> Can you try to use mdout_analyzer.py in AmberTools15? (It's pain to
> >>>>>> debug
> >>>>>> Perl code)
> >>>>>>
> >>>>>> Check http://ambermd.org/doc12/Amber15.pdf (page 515)
> >>>>>>
> >>>>>> Hai
> >>>>>>
> >>>>>> On Sat, Mar 19, 2016 at 1:25 AM, Sehrish Naz Aijaz <
> >>>>>> sehrish.naz.outlook.com
> <javascript:_e(%7B%7D,'cvml','sehrish.naz.outlook.com');>>
> >>>>>> wrote:
> >>>>>>
> >>>>>>> Dear all,
> >>>>>>> I had run 10 ns simulation (AMBER12) of large compounds in TIP3P
> box
> >>>>>>> to
> >>>>>>> check their stable conformation with time. the input file I used
> for
> >>>>>>> production is
> >>>>>>> NPT production with no restrains
> >>>>>>> &cntrl
> >>>>>>> imin=0, ntx=7, irest=1, ntrx=1, ntxo=1,
> >>>>>>> ntpr=500, ntwx=500, ntwv=200, ntwe=200,
> >>>>>>> ntf=2, ntb=2, cut=10.0,
> >>>>>>> nsnb=100, igb=0,
> >>>>>>> nstlim=2000000,
> >>>>>>> t=0.0, dt=0.001,
> >>>>>>> ntt=3, gamma_ln=1.0, tempi=300.0, temp0=300.0,
> >>>>>>> vlimit=20,
> >>>>>>> ntp=1, taup=1.0, pres0=1.0, comp=44.6,
> >>>>>>> ntc=2, tol=0.00000001,
> >>>>>>> /
> >>>>>>>
> >>>>>>> after getting the production files. I tried to calculate the total
> >>>>>>> energy
> >>>>>>> graphs of the system by using perl script as follows
> >>>>>>> . #!/usr/bin/perl
> >>>>>>>
> >>>>>>>
> >>>>>>> if ($#ARGV < 0) {
> >>>>>>> print " Incorrect usage...\n";
> >>>>>>> exit;
> >>>>>>> }
> >>>>>>>
> >>>>>>>
> >>>>>>> foreach $i ( 0..$#ARGV ) {
> >>>>>>> $filein = $ARGV[$i];
> >>>>>>> $checkfile = $filein;
> >>>>>>> $checkfile =~ s/\.Z//;
> >>>>>>> if ( $filein ne $checkfile ) {
> >>>>>>> open(INPUT, "zcat $filein |") ||
> >>>>>>> die "Cannot open compressed $filein -- $!\n";
> >>>>>>> } else {
> >>>>>>> open(INPUT, $filein) || die "Cannot open $filein -- $!\n";
> >>>>>>> }
> >>>>>>> print "Processing sander output file ($filein)...\n";
> >>>>>>> &process_input;
> >>>>>>> close(INPUT);
> >>>>>>> }
> >>>>>>>
> >>>>>>> print "Starting output...\n";
> >>>>>>> .sortedkeys = sort by_number keys(%TIME);
> >>>>>>> .sortedavgkeys = sort by_number keys(%AVG_TIME);
> >>>>>>>
> >>>>>>> foreach $i ( TEMP, TSOLUTE, TSOLVENT, PRES, EKCMT, ETOT, EKTOT,
> EPTOT,
> >>>>>>> DENSITY, VOLUME, ESCF ) {
> >>>>>>> print "Outputing summary.$i\n";
> >>>>>>> open(OUTPUT, "> summary.$i");
> >>>>>>> %outarray = eval "\%$i";
> >>>>>>> foreach $j ( .sortedkeys ) {
> >>>>>>> print OUTPUT "$j ", $outarray{$j}, "\n";
> >>>>>>> }
> >>>>>>> close (OUTPUT);
> >>>>>>>
> >>>>>>> print "Outputing summary_avg.$i\n";
> >>>>>>> open(OUTPUT, "> summary_avg.$i");
> >>>>>>> %outarray = eval "\%AVG_$i";
> >>>>>>> foreach $j ( .sortedavgkeys ) {
> >>>>>>> print OUTPUT "$j ", $outarray{$j}, "\n";
> >>>>>>> }
> >>>>>>> close (OUTPUT);
> >>>>>>>
> >>>>>>> print "Outputing summary_rms.$i\n";
> >>>>>>> open(OUTPUT, "> summary_rms.$i");
> >>>>>>> %outarray = eval "\%RMS_$i";
> >>>>>>> foreach $j ( .sortedavgkeys ) {
> >>>>>>> print OUTPUT "$j ", $outarray{$j}, "\n";
> >>>>>>> }
> >>>>>>> close (OUTPUT);
> >>>>>>>
> >>>>>>>
> >>>>>>> }
> >>>>>>>
> >>>>>>>
> >>>>>>> sub by_number {
> >>>>>>> if ($a < $b) {
> >>>>>>> -1;
> >>>>>>> } elsif ($a == $b) {
> >>>>>>> 0;
> >>>>>>> } elsif ($a > $b) {
> >>>>>>> 1;
> >>>>>>> }
> >>>>>>> }
> >>>>>>>
> >>>>>>> sub process_input {
> >>>>>>>
> >>>>>>> $status = 0;
> >>>>>>> $debug = 0;
> >>>>>>> while ( <INPUT> ) {
> >>>>>>> $string = $_;
> >>>>>>>
> >>>>>>> print $_ if ( ! /NB-upda/ && $debug );
> >>>>>>>
> >>>>>>> if (/A V E R A G E S/) {
> >>>>>>> $averages = 1;
> >>>>>>> ($averages_over) = /.*O V E R.*(\d*).*S T E P S/;
> >>>>>>> }
> >>>>>>>
> >>>>>>> $rms = 1 if (/R M S/);
> >>>>>>>
> >>>>>>> if (/NSTEP/) {
> >>>>>>> ($time, $temp, $pres) =
> >>>>>>> /NSTEP =.*TIME.* =(.*\d*\.\d*).*TEMP.*
> =(.*\d*\.\d*).*PRESS =
> >>>>>>> (.*\d*\.\d*)/;
> >>>>>>> if ( $debug ) {
> >>>>>>> print $_;
> >>>>>>> print "time is $time, temp is $temp, pres is $pres\n";
> >>>>>>> }
> >>>>>>> $_ = <INPUT>;
> >>>>>>>
> >>>>>>> if (/Etot/) {
> >>>>>>> ($etot, $ektot, $eptot) =
> >>>>>>>
> >>>>>>> /Etot.*=(.*\d*\.\d*).*EKtot.*=(.*\d*\.\d*).*EPtot.*=(.*\d*\.\d*)/;
> >>>>>>> if ( $debug ) {
> >>>>>>> print $_;
> >>>>>>> print "Etot is $etot, ektot is $ektot, eptot is
> $eptot\n";
> >>>>>>> }
> >>>>>>> $_ = <INPUT>;
> >>>>>>> }
> >>>>>>> if (/BOND.*ANGLE.*DIHED/) {
> >>>>>>> ($bond, $angle, $dihedral) =
> >>>>>>>
> >>>>>>> /BOND.*=(.*\d*\.\d*).*ANGLE.*=(.*\d*\.\d*).*DIHED.*=(.*\d*\.\d*)/;
> >>>>>>> if ( $debug ) {
> >>>>>>> print $_;
> >>>>>>> print "bond is $bond, angle is $angle, dihedral is
> >>>>>>> $dihedral\n";
> >>>>>>> }
> >>>>>>> $_ = <INPUT>;
> >>>>>>> }
> >>>>>>> if (/1-4 NB/) {
> >>>>>>> ($nb14, $eel14, $nb) =
> >>>>>>> /1-4 NB.*=(.*\d*\.\d*).*1-4
> >>>>>>> EEL.*=(.*\d*\.\d*).*VDWAALS.*=(.*\d*\.\d*)/;
> >>>>>>> if ( $debug ) {
> >>>>>>> print $_;
> >>>>>>> print "nb14 is $nb14, eel14 is $eel14, vdwaals is
> $nb\n";
> >>>>>>> }
> >>>>>>> $_ = <INPUT>;
> >>>>>>> }
> >>>>>>> if (/EELEC/) {
> >>>>>>> ($eel, $ehbond, $constraint) =
> >>>>>>>
> >>>>>>>
> >>>>>>>
> /EELEC.*=(.*\d*\.\d*).*EHBOND.*=(.*\d*\.\d*).*CONSTRAINT.*=(.*\d*\.\d*)/;
> >>>>>>> if ( $debug ) {
> >>>>>>> print $_;
> >>>>>>> print "eel is $eel, ehbond is $ehbond, constraint is
> >>>>>>> $constraint\n";
> >>>>>>> }
> >>>>>>> $_ = <INPUT>;
> >>>>>>> #
> >>>>>>> # check to see if EAMBER is in the mdout file
> (present
> >>>>>>> when
> >>>>>>> # NTR=1)
> >>>>>>> #
> >>>>>>> if ( /EAMBER/ ) {
> >>>>>>> $_ = <INPUT>;
> >>>>>>> }
> >>>>>>> }
> >>>>>>> if (/EKCMT/) {
> >>>>>>> ($ekcmt, $virial, $volume) =
> >>>>>>>
> >>>>>>>
> /EKCMT.*=(.*\d*\.\d*).*VIRIAL.*=(.*\d*\.\d*).*VOLUME.*=(.*\d*\.\d*)/;
> >>>>>>> if ( $debug ) {
> >>>>>>> print $_;
> >>>>>>> print "Ekcmt is $ekcmt, virial is $virial, volume is
> >>>>>>> $volume\n";
> >>>>>>> }
> >>>>>>> $_ = <INPUT>;
> >>>>>>> }
> >>>>>>> if (/T_SOLUTE/) {
> >>>>>>> ($tsolute, $tsolvent) =
> >>>>>>> /T_SOLUTE =(.*\d*\.\d*).*T_SOLVENT =(.*\d*\.\d*)/;
> >>>>>>> if ( $debug ) {
> >>>>>>> print $_;
> >>>>>>> print "Temp solute is $tsolute, temp solvent is
> >>>>>>> $tsolvent\n";
> >>>>>>> }
> >>>>>>> $_ = <INPUT>;
> >>>>>>> }
> >>>>>>>
> >>>>>>> if (/Density/) {
> >>>>>>> ($density) = /.*Density.*=(.*\d*\.\d*)/;
> >>>>>>> if ( $debug ) {
> >>>>>>> print $_;
> >>>>>>> print "Density is $density\n";
> >>>>>>> }
> >>>>>>> $_ = <INPUT>;
> >>>>>>> }
> >>>>>>>
> >>>>>>> if (/Etot/) {
> >>>>>>> ($etot, $ektot, $eptot) =
> >>>>>>>
> >>>>>>> /Etot.*=(.*\d*\.\d*).*EKtot.*=(.*\d*\.\d*).*EPtot.*=(.*\d*\.\d*)/;
> >>>>>>> if ( $debug ) {
> >>>>>>> print $_;
> >>>>>>> print "Etot is $etot, ektot is $ektot, eptot is
> $eptot\n";
> >>>>>>> }
> >>>>>>> $_ = <INPUT>;
> >>>>>>> }
> >>>>>>> if (/ESCF/) {
> >>>>>>> ($escf) =
> >>>>>>> /.*ESCF.*=(.*\d*\.\d*)/;
> >>>>>>> if ( $debug ) {
> >>>>>>> print $_;
> >>>>>>> print "ESCF is $escf\n";
> >>>>>>> }
> >>>>>>> $_ = <INPUT>;
> >>>>>>> }
> >>>>>>>
> >>>>>>> # update arrays
> >>>>>>>
> >>>>>>> if ( $averages == 1 ) {
> >>>>>>> $AVG_TIME{$time} = $time;
> >>>>>>> $AVG_TEMP{$time} = $temp;
> >>>>>>> $AVG_PRES{$time} = $pres;
> >>>>>>> $AVG_ETOT{$time} = $etot;
> >>>>>>> $AVG_EKTOT{$time} = $ektot;
> >>>>>>> $AVG_EPTOT{$time} = $eptot;
> >>>>>>> $AVG_BOND{$time} = $bond;
> >>>>>>> $AVG_ANGLE{$time} = $angle;
> >>>>>>> $AVG_DIHEDRAL{$time} = $dihedral;
> >>>>>>> $AVG_NB14{$time} = $nb14;
> >>>>>>> $AVG_EEL14{$time} = $eel14;
> >>>>>>> $AVG_NB{$time} = $nb;
> >>>>>>> $AVG_EEL{$time} = $eel;
> >>>>>>> $AVG_EHBOND{$time} = $ehbond;
> >>>>>>> $AVG_CONSTRAINT{$time} = $constraint;
> >>>>>>> $AVG_EKCMT{$time} = $ekcmt;
> >>>>>>> $AVG_VIRIAL{$time} = $virial;
> >>>>>>> $AVG_VOLUME{$time} = $volume;
> >>>>>>> $AVG_TSOLUTE{$time} = $tsolute;
> >>>>>>> $AVG_TSOLVENT{$time} = $tsolvent;
> >>>>>>> $AVG_DENSITY{$time} = $density;
> >>>>>>> $AVG_ESCF{$time} = $escf;
> >>>>>>> $averages = 0;
> >>>>>>> } elsif ( $rms == 1 ) {
> >>>>>>> $RMS_TIME{$time} = $time;
> >>>>>>> $RMS_TEMP{$time} = $temp;
> >>>>>>> $RMS_PRES{$time} = $pres;
> >>>>>>> $RMS_ETOT{$time} = $etot;
> >>>>>>> $RMS_EKTOT{$time} = $ektot;
> >>>>>>> $RMS_EPTOT{$time} = $eptot;
> >>>>>>> $RMS_BOND{$time} = $bond;
> >>>>>>> $RMS_ANGLE{$time} = $angle;
> >>>>>>> $RMS_DIHEDRAL{$time} = $dihedral;
> >>>>>>> $RMS_NB14{$time} = $nb14;
> >>>>>>> $RMS_EEL14{$time} = $eel14;
> >>>>>>> $RMS_NB{$time} = $nb;
> >>>>>>> $RMS_EEL{$time} = $eel;
> >>>>>>> $RMS_EHBOND{$time} = $ehbond;
> >>>>>>> $RMS_CONSTRAINT{$time} = $constraint;
> >>>>>>> $RMS_EKCMT{$time} = $ekcmt;
> >>>>>>> $RMS_VIRIAL{$time} = $virial;
> >>>>>>> $RMS_VOLUME{$time} = $volume;
> >>>>>>> $RMS_TSOLUTE{$time} = $tsolute;
> >>>>>>> $RMS_TSOLVENT{$time} = $tsolvent;
> >>>>>>> $RMS_DENSITY{$time} = $density;
> >>>>>>> $RMS_ESCF{$time} = $escf;
> >>>>>>>
> >>>>>>> $rms = 0;
> >>>>>>> } else {
> >>>>>>> $TIME{$time} = $time;
> >>>>>>> $TEMP{$time} = $temp;
> >>>>>>> $PRES{$time} = $pres;
> >>>>>>> $ETOT{$time} = $etot;
> >>>>>>> $EKTOT{$time} = $ektot;
> >>>>>>> $EPTOT{$time} = $eptot;
> >>>>>>> $BOND{$time} = $bond;
> >>>>>>> $ANGLE{$time} = $angle;
> >>>>>>> $DIHEDRAL{$time} = $dihedral;
> >>>>>>> $NB14{$time} = $nb14;
> >>>>>>> $EEL14{$time} = $eel14;
> >>>>>>> $NB{$time} = $nb;
> >>>>>>> $EEL{$time} = $eel;
> >>>>>>> $EHBOND{$time} = $ehbond;
> >>>>>>> $CONSTRAINT{$time} = $constraint;
> >>>>>>> $EKCMT{$time} = $ekcmt;
> >>>>>>> $VIRIAL{$time} = $virial;
> >>>>>>> $VOLUME{$time} = $volume;
> >>>>>>> $TSOLUTE{$time} = $tsolute;
> >>>>>>> $TSOLVENT{$time} = $tsolvent;
> >>>>>>> $DENSITY{$time} = $density;
> >>>>>>> $ESCF{$time} = $escf;
> >>>>>>> }
> >>>>>>>
> >>>>>>> }
> >>>>>>> }
> >>>>>>> }
> >>>>>>>
> >>>>>>> But after running this perl script on the output files I got graph
> >>>>>>> displaying half values of output files as attached here. Can
> anybody
> >>>>>> guide
> >>>>>>> me whats wrong with the perl graph or my input file as my output
> files
> >>>>>> are
> >>>>>>> printing all values for energy but perl script plot half values???
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Sent from Mail for Windows 10
> >>>>>>>
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> AMBER mailing list
> >>>>>>> AMBER.ambermd.org
> <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>
> >>>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>> --
> >>> -------------------------
> >>> Daniel R. Roe, PhD
> >>> Department of Medicinal Chemistry
> >>> University of Utah
> >>> 30 South 2000 East, Room 307
> >>> Salt Lake City, UT 84112-5820
> >>> http://home.chpc.utah.edu/~cheatham/
> >>> (801) 587-9652
> >>> (801) 585-6208 (Fax)
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:_e(%7B%7D,'cvml','AMBER.ambermd.org');>
> http://lists.ambermd.org/mailman/listinfo/amber
>

-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Mar 28 2016 - 07:00:03 PDT