Hi, i'm using umbrella sampling and i'm a beginner in GROMACS.
as an example i got 5 dist.xvg files and then: >>command: perl distances.pl this is distances.pl: #!/usr/bin/perl -w use strict; # write output to single file open(OUT, ">>summary_distances.dat"); for (my $j=0; $j<=5; $j++) { open(IN, "<dist${j}.xvg"); my @array = <IN>; my $distance; foreach $_ (@array) { if ($_ =~ /[#@]/) { # do nothing, it's a comment or formatting line } else { my @line = split(" ", $_); $distance = $line[1]; } } close(IN); print OUT "$j\t$distance\n"; } close(OUT); # clean up print "Cleaning up...\n"; for (my $k=0; $k<=5; $k++) { unlink "dist${k}.xvg"; } exit; but summary-distances.dat: 0 0.382 1 0.382 0 0.382 1 0.382 2 0.382 3 0.382 4 0.382 5 0.382 ~ ~ ~ 0.382 is just the first number in dist.xvg files; for example dist0.xvg is: # This file was created Sat Nov 25 04:47:25 2017 # Created by: # :-) GROMACS - gmx distance, VERSION 5.1.4 (-: # # Executable: /usr/local/gromacs/bin/gmx # Data prefix: /usr/local/gromacs # Command line: # gmx distance -s pull.tpr -f conf0.gro -n index.ndx -oall dist0.xvg # gmx distance is part of G R O M A C S: # # ¸Â°<88><96><91><98>ò<90><91><8c><8b><9a><8d><8c>þ<91><9b>ü<93><90><91><96><91><98>ì<97><8d><96><92><8f><8c> # @ title "Distance" @ xaxis label "Time (ps)" @ yaxis label "Distance (nm)" @TYPE xy 0.000 0.382 0.382 0.383 0.383 0.383 0.383 1.178 0.382 0.382 0.383 0.383 0.383 0.383 0.383 0.382 0.818 0.382 0.382 0.382 0.382 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.382 0.382 0.383 0.383 0.383 0.383 1.178 0.382 0.382 0.383 0.383 0.383 0.383 0.383 0.382 0.818 0.382 0.382 0.382 0.382 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.151 0.237 0.160 0.242 0.123 0.147 ~ ~ what is my mistake?is that perl script or?! or because of i selected very close conf.gro files (0-5)? i selected them just for testing my script and to tell the truth i didn't know how use gmx distance to get all 718 (configuration's) xvg files with just ONE command so i have to get .xvg files one by one.(would you please tell me?) - it's much similar to tutorial's(by Mr Lemkul) perl script but not as same as it because i got some errors so i had to use gmx distance separately. Best Regards Rose -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.