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>
>> 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
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>>>>>>
>>>>> _______________________________________________
>>>>> 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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>>>
>>> --
>>> -------------------------
>>> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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Received on Thu Mar 24 2016 - 23:00:04 PDT
