On 11/25/17 12:57 PM, rose rahmani wrote:
On Sat, Nov 25, 2017 at 7:01 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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.
first, when you open script file in browser ,then copy it and paste it to
Linux, all lines will be started with "#" which makes all scripts
inactive.That was a carelessness personally from me ;)))
Right-click, save as. Don't open or manipulate the script in a browser.
- When i use your script,
a) i need to change 1-Chain_A 2-Chain_B 3- number"500"
b) perl distances.pl
c) Processing configuration 0...
Processing configuration 1...
Processing configuration 2...
Processing configuration 3...
Processing configuration 4...
Processing configuration 5...
readline() on closed filehandle IN at distances.pl line 14.
Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 28.
This and the errors that follow mean the script can't find a file to
open. I'm not sure all of what you've changed in the script, because if
truly you are only trying to process six files (indices 0-5), then this
shouldn't happen.
readline() on closed filehandle IN at distances.pl line 14.
Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 28.
readline() on closed filehandle IN at distances.pl line 14.
Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 28.
readline() on closed filehandle IN at distances.pl line 14.
Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 28.
readline() on closed filehandle IN at distances.pl line 14.
Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 28.
readline() on closed filehandle IN at distances.pl line 14.
Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 28.
i think this is the common error for most of us.Because of this, as i said
i had to run gmx distance separately and delete these lines from perl
scripts( which you suggested).it worked,but my problem is why my
summarydistances.dat is like this:
0 0.382
1 0.382
2 0.382
3 0.382
4 0.382
5 0.382
~
Oh!!!! yes you're right. Although i choose groups which i need to calculate
distances,BUT they didn't actually move as i expected and i've been
intending and looking for from the first!
This is the first problem you should solve. Running these
post-processing scripts is a waste of time if your simulation didn't act
as you expected it.
?-if you remember yesterday i told that the protein in getting closer to
wall instead of ZnO!! (protein is between ZnO and wall) ,while i'm trying
to calculate different distances between ZnO and Protein!!!! and i asked
which part of my work may be wrong?it means that protein tends to wall more
than ZnO????
More likely, your .mdp settings were wrong. Please post (do not attach)
the contents of your .mdp file.
?- and what i don't undrstand is that how perl script calculate just "one"
value from xvg file which contain many values?i cant understand.
When gmx distance is executed properly on a single coordinate file,
there can (by definition) be only one COM distance between two groups.
If you're getting anything else, you're using gmx distance wrong. Run it
interactively to be sure you understand the syntax and can execute the
command and get a sensible result before layering on the complexity of
my processing script.
-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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