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
>>>>
>>>>
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
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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)
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Received on Mon Mar 21 2016 - 08:00:03 PDT
