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
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>>>>> AMBER mailing list
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>>>>>
>>>> _______________________________________________
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>>>
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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
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Received on Thu Mar 24 2016 - 23:00:03 PDT
