/usr/bin/demux is in gromacs 2016.1-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 | #!/usr/bin/perl -w
# in: input filename
$in = shift || die("Please specify input filename");
# If your exchange was every N ps and you saved every M ps you can make for
# the missing frames by setting extra to (N/M - 1). If N/M is not integer,
# you're out of luck and you will not be able to demux your trajectories at all.
$extra = shift || 0;
$ndx = "replica_index.xvg";
$temp = "replica_temp.xvg";
@comm = ("-----------------------------------------------------------------",
"Going to read a file containing the exchange information from",
"your mdrun log file ($in).",
"This will produce a file ($ndx) suitable for",
"demultiplexing your trajectories using trjcat,",
"as well as a replica temperature file ($temp).",
"Each entry in the log file will be copied $extra times.",
"-----------------------------------------------------------------");
for($c=0; ($c<=$#comm); $c++) {
printf("$comm[$c]\n");
}
# Open input and output files
open (IN_FILE,"$in") || die ("Cannot open input file $in");
open (NDX,">$ndx") || die("Opening $ndx for writing");
open (TEMP,">$temp") || die("Opening $temp for writing");
sub pr_order {
my $t = shift;
my $nrepl = shift;
printf(NDX "%-20g",$t);
for(my $k=0; ($k<$nrepl); $k++) {
my $oo = shift;
printf(NDX " %3d",$oo);
}
printf(NDX "\n");
}
sub pr_revorder {
my $t = shift;
my $nrepl = shift;
printf(TEMP "%-20g",$t);
for(my $k=0; ($k<$nrepl); $k++) {
my $oo = shift;
printf(TEMP " %3d",$oo);
}
printf(TEMP "\n");
}
$nrepl = 0;
$init = 0;
$tstep = 0;
$nline = 0;
$tinit = 0;
while ($line = <IN_FILE>) {
chomp($line);
if (index($line,"init_t") >= 0) {
@log_line = split (' ',$line);
$tinit = $log_line[2];
}
if (index($line,"Repl") == 0) {
@log_line = split (' ',$line);
if (index($line,"There") >= 0) {
$nrepl = $log_line[3];
}
elsif (index($line,"time") >= 0) {
$tstep = $log_line[6];
}
elsif ((index($line,"Repl ex") == 0) && ($nrepl == 0)) {
# Determine number of replicas from the exchange information
printf("%s\n%s\n",
"WARNING: I did not find a statement about number of replicas",
"I will try to determine it from the exchange information.");
for($k=2; ($k<=$#log_line); $k++) {
if ($log_line[$k] ne "x") {
$nrepl++;
}
}
}
if (($init == 0) && ($nrepl > 0)) {
printf("There are $nrepl replicas.\n");
@order = ();
@revorder = ();
for($k=0; ($k<$nrepl); $k++) {
$order[$k] = $k;
$revorder[$k] = $k;
}
for($ee=0; ($ee<=$extra); $ee++) {
pr_order($tinit+$ee,$nrepl,@order);
pr_revorder($tinit+$ee,$nrepl,@revorder);
$nline++;
}
$init = 1;
}
if (index($line,"Repl ex") == 0) {
$k = 0;
for($m=3; ($m<$#log_line); $m++) {
if ($log_line[$m] eq "x") {
$revorder[$order[$k]] = $k+1;
$revorder[$order[$k+1]] = $k;
$tmp = $order[$k];
$order[$k] = $order[$k+1];
$order[$k+1] = $tmp;
# printf ("Swapping %d and %d on line %d\n",$k,$k+1,$line_number);
}
else {
$k++;
}
}
for($ee=0; ($ee<=$extra); $ee++) {
pr_order($tstep+$ee,$nrepl,@order);
pr_revorder($tstep+$ee,$nrepl,@revorder);
$nline++;
}
}
}
}
close IN_FILE;
close NDX;
close TEMP;
printf ("Finished writing $ndx and $temp with %d lines\n",$nline);
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