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

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 29 Mar 2016 05:57:25 -0400

> On Mar 29, 2016, at 12:03 AM, Sehrish Naz Aijaz <sehrish.naz.outlook.com> wrote:
>
> Sorry to say but I did not receive any mail from your side that’s why I again ask for help...

Check your spam or junk folder and see if your mail client filtered it. If so, fix your settings so emails from ambermd.org are not filtered.

>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>
> From: Daniel Roe<mailto:daniel.r.roe.gmail.com>
> Sent: 28 March 2016 18:37
> To: Sehrish Naz Aijaz<mailto:sehrish.naz.outlook.com>; AMBER Mailing List<mailto:amber.ambermd.org>
> Subject: Re: [AMBER] problem in plotting total energy graphs by perl script
>
> 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

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Received on Tue Mar 29 2016 - 03:30:03 PDT