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

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 25 Mar 2016 08:48:40 -0600

Hi,

Two things I need to mention here. First, if you want the data from
multiple files with a single 'readdata' command concatenated in this
version of cpptraj, you need to name the data sets with the 'name'
keyword (this behavior is fixed in the upcoming release). Second is
that when writing your output data file you forgot the '[*]' (see my
original example). When you read in the data, each individual energy
component is given an 'aspect', e.g. [Etot] for total energy, [EPtot]
for total potential energy. You can test what data sets are selected
by what expression with the 'selectds' command. See Chapter 29.2 'Data
Sets and Data Files' of the Amber15 manual for more details.

So in your case you probably want the following:

readdata 32a_prod?.out name MyData
writedata energy.agr MyData[*]

Hope this helps,

-Dan

On Thu, Mar 24, 2016 at 10:59 PM, Sehrish Naz Aijaz
<sehrish.naz.outlook.com> 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>
> Sent: 22 March 2016 21:01
> Cc: AMBER Mailing List<mailto: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> 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> 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>
>>> Sent: 20 March 2016 01:11
>>> To: AMBER Mailing List<mailto: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>
>>>> Sent: 19 March 2016 14:48
>>>> To: AMBER Mailing List<mailto: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>
>>>> 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>
>>>>> Sent: 19 March 2016 13:56
>>>>> To: AMBER Mailing List<mailto: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>
>>>>> 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
>>>>>> 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
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> _______________________________________________
>>>> AMBER mailing list
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
>>> AMBER mailing list
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>>> 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
>
>
>
> --
> -------------------------
> 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
> _______________________________________________
> AMBER mailing list
> 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 Fri Mar 25 2016 - 08:00:06 PDT