Mark Abraham wrote:
David van der Spoel wrote:
xi zhao wrote:
Sorry, but in source of v3.3.2 and 3.3.1 of the website , there is
not demux.pl
src/contrib/scripts
You're dead right.
WIll fix this for the next release. It is attached to this mail.
Actually, Xi Zhao is right here, David. Neither of the 3.3.1 or 3.3.2
source distributions has either this subdirectory or demux.pl anywhere
else.
Presumably the CVS distribution will have it, if you want to try
downloading that, Xi. See http://wiki.gromacs.org/index.php/CVS_HowTo
Mark
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#!/usr/bin/perl -w
# $Id: demux.pl,v 1.1.2.4 2007/01/16 12:03:48 spoel Exp $
# 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 $nrepl = shift;
printf(NDX "%-8g",$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 $nrepl = shift;
printf(TEMP "%-8g",$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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