On 11/3/18 2:15 PM, rose rahmani wrote:
On Sat, 3 Nov 2018, 19:56 Justin Lemkul <jalem...@vt.edu wrote:
On 11/2/18 11:36 AM, rose rahmani wrote:
but this is output of -oall. its not a single value?!
You are asking in your command for all interatomic distances between the
groups (presumably, because you haven't shown your selection). This
command won't yield what you're hoping to see and my advice does not
apply for this type of situation (which doesn't seem to even match your
original statement of your problem).
gmx distance -f md2.xtc -oall dist.xvg -n index.ndx
# gmx distance is part of G R O M A C S:
#
#
¸<8d><9a><9a><91>ÃÂ<9a><9b>ð<8d><9e><91><98><9a>ò<9e><98><9a><91><8b><9e>þ<85><8a><8d><9a>ü<86><9e><91>ì<94><86><9d><99a>8a><<
#
@ title "Distance"
@ xaxis label "Time (ps)"
@ yaxis label "Distance (nm)"
@TYPE xy
1.000 0.229 0.229 0.446 0.582 0.446 0.229 0.446
0.583 0.447 0.229 0.447 0.227 0.228 0.229 0.446
0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447
0.227 0.227 0.228 0.446 0.582 0.446 0.227 0.446
0.583 0.447 0.227 0.447 0.227 0.228 0.229 0.446
0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447
0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446
0.583 0.447 0.228 0.447 0.227 0.229 0.229 0.446
0.582 0.446 0.229 0.446 0.583 0.447 0.229 0.447
0.227 0.229 0.229 0.446 0.582 0.446 0.229 0.446
0.583 0.447 0.229 0.447 0.227 0.228 0.229 0.446
0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447
0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446
0.583 0.447 0.228 0.447 0.227 0.227 0.228 0.446
0.582 0.446 0.227 0.446 0.583 0.447 0.227 0.447
0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446
0.583 0.447 0.228 0.4
.
.
.
and this is -o of g_dist;
g_dist -f md2.xtc -s md2.tpr -n index -o all.xvg
#
# g_dist is part of G R O M A C S:
#
# GRowing Old MAkes el Chrono Sweat
#
@ title "Distance"
@ xaxis label "Time (ps)"
@ yaxis label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
0.0000000 0.2176011 -0.0120678 -0.0465498 0.2122209
1.0000000 0.2124534 -0.0301750 -0.0463870 0.2051198
2.0000000 0.1923753 -0.0158403 -0.0510135 0.1848106
3.0000000 0.1885315 -0.0107298 -0.0488160 0.1817856
4.0000000 0.2044982 -0.0052650 -0.0490329 0.1984630
5.0000000 0.2033602 -0.0002742 -0.0429537 0.1987720
6.0000000 0.2050487 0.0013833 -0.0444658 0.2001646
7.0000000 0.2002475 0.0041072 -0.0415003 0.1958568
8.0000000 0.2006473 0.0033450 -0.0511889 0.1939790
9.0000000 0.2032918 -0.0000119 -0.0330052 0.2005947
10.0000000 0.2255659 0.0003929 -0.0415857 0.2216990
11.0000000 0.2243811 0.0118313 -0.0344751 0.2214010
12.0000000 0.2347855 0.0078275 -0.0383532 0.2314994
13.0000000 0.2371541 0.0081918 -0.0388267 0.2338107
Here, you have what you want (I assume), and the first column after the
time is all you need. It's the distance, which also can't be negative
because it is the magnitude of the vector length and is unsigned.
How S0 is calculated? Does it resulted from distance between COM of amino
acid and COM of tube? Although, it is the magnitude of ... but it's
The distance you get is the distance you ask for in your selection
(which isn't shown or stated). The distance formula is quite simple,
consult any geometry textbook.
calculated from x,y,z which may be negative and were not abaolute?! In
addition, i put AAs (more than) 1.5 nm far from tube as an initial
configuration, but any 1.5 nm distance..???
A component of a vector may be positive or negative, these are just
differences along x, y, and z. The total length of a vector is a
magnitude and is therefore positive.
-Justin
-Justin
.
.
.
On Thu, Nov 1, 2018 at 11:39 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 11/1/18 2:25 PM, rose rahmani wrote:
I don't know how? I mean x,y,z(s1, s2,s3) in dist.xvg can easily be
multiplied by (-), but how should i modify second column,i don't know
how
s0 is calculated by g_distance to modify it??
The output of -oall is a single value, the actual distance, which I
assume is what you are talking about in your previous message. You can
parse that column in any scripting language you like and
[ pseudocode, not functional ]
if (value < 0)
{
value *= -1
}
-Justin
On Wed, 31 Oct 2018, 19:38 Justin Lemkul, <jalem...@vt.edu> wrote:
On 10/31/18 12:06 PM, rose rahmani wrote:
Hi,
I want to calculate distances between fixed tube in the middle of the
box
and amino acids(all are same type)around it. But gmx distance gives
me
the
relative distance i mean AA can be front or back( can be 0.5 or -0.5
from
tube) of tube but still |-0.5|=0.5 nm far from it. How can i have
the
absolute value of distances?
Would you please help me?
Write a simple post-processing script that multiplies any negative
value
by -1.
-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.thelemkullab.com
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==================================================
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.thelemkullab.com
==================================================
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--
==================================================
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.thelemkullab.com
==================================================
--
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* Please search the archive at
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posting!
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send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
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.thelemkullab.com
==================================================
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