Please resend your email with proper format. It's impossible for me to read
your email and your script.
Hai
On Sat, Mar 19, 2016 at 1:20 AM, Sehrish Naz Aijaz <sehrish.naz.outlook.com>
wrote:
>
>
> Sent from Mail for Windows 10
>
> From: Sehrish Naz
> Sent: 19 March 2016 13:16
> To: sehrish.naz.outlook.com
> Subject: problem in plotting total energy graph by using perl script
>
> Dear all,I had run 10 ns simulation 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/perlif ($#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??? Regards,
> Sehrish Naz
> Jr. Research Fellow,Computational Chemistry Unit.
> Dr. Panjwani Center for Molecular Medicine and Drug Research,
> International Center for Chemical and Biological Sciences,
> University of Karachi, Karachi-75270.
> E-mail: mjazse.gmail.com
>
>
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Received on Sat Mar 19 2016 - 01:30:04 PDT
