On 11/25/17 5:05 AM, rose rahmani wrote:
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)?
My Perl script expects each file to have *one* value in it, the COM
distance between two chosen groups. Your output seems to be something
else entirely, suggesting you didn't choose appropriate groups.
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?)
You don't. Run have to calculate each separately (trivial in a shell or
other script loop), or otherwise just analyze the trajectory, get one
time series, and do your own parsing.
- 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.
If you can tell me what the actual error are, I can help sort those out.
As I said before, I have often heard "your script doesn't work" and then
no one actually follows up to tell me why. If you're getting errors, I'd
like to know so I can actually provide a solution.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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