tekle...@ualberta.ca wrote:
Dear Justine,
I got it and works fine.
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000000 0.7047197 -0.3054392 -0.1559912 0.6156325
19002.0000000 0.7591453 -0.2601027 -0.2659363 0.6617599
19004.0000000 0.7763510 -0.3043177 -0.2214912 0.6790090
19006.0000000 0.7837191 -0.2325068 -0.2653693 0.6998110
=============================
I have another question for you. Does g_analyse is oky to use to get the
mean separation.
I don't see why not. That's pretty much the main function of g_analyze.
g_anayze -f XXXX.xvg -av average.xvg -errbar enum -b 19000 -e 20000
is the column 1 and two is correct means time and distance respectively.
Per the notation in the .xvg file, yes.
=========================
Is the same process apply for the g-rdf?
Group 0 ( System) has 28708 elements
Group 1 ( PAP) has 512 elements
Group 2 ( HEP) has 28196 elements
Group 3 ( RING) has 20 elements
I want to calculate g(r) for PAP molecules...... but by default it is
there does I need to create two PAP_1 and PAP_2 to get the g(r). To get
for the
PAP-PAP g(r) value. Or just need to select 1 twice?
Try it and see :)
-Justin
Rob
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
tekle...@ualberta.ca wrote:
Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3
(single precision)
Group 0 ( System) has 28708 elements
Group 1 ( PAP) has 512 elements
Group 2 ( HEP) has 28196 elements
Group 3 ( RING) has 20 elements
Select a group: 3
Selected 3: 'RING'
Select a group: 3
Selected 3: 'RING'
Reading frame 0 time 19000.000
Back Off! I just backed up DistPAP8HEP.xvg to ./#DistPAP8HEP.xvg.8#
Last frame 500 time 20000.000
====================
which means I have to create two index file for two rings Ring_1 AND
Ring_2 and choose both of them. If I am correct.
Yes. Otherwise the distance from the center of mass of RING is
calculated relative to the center of mass of RING, which by definition
will always be zero.
-Justin
Rob
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
tekle...@ualberta.ca wrote:
The following is the out put.
# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 20000
-o DistPAP8HEP.xvg
#
# /home/software/gromacs/3.3.3/bin/g_dist is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@ 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"
19000.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19002.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19004.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19006.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19008.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19010.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19012.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19014.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19016.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19018.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19020.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19022.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19024.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19026.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19028.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19030.0000000 0.0000000 0.0000000 0.0000000 0.0000000
19032.0000000 0.0000000 0.00000
You say you want the distance between two rings, but you only showed
an index group for one of them (presumably), and the fact that
you've gotten all zeroes as a result would suggest that you chose
the same group twice for the distance calculation. Which groups did
you select? Do they correspond to two, non-overlapping index groups?
-Justin
Quoting tekle...@ualberta.ca:
Dear Gromacs users,
I run my simulation for 20ns and want to extract aromatic-aromatic
distance to see the stacking issue. But I am unable to get the value.
I have 24 molecules in my simulation and filled with solvents.
My index file is like that:
[ System ]
1 2 3 4 5 6 7 8 9 10 11 12 13
14 15
16 17 18 19 20 21 22 23 24 25 26 27 28
29 30
31 32 33 34 35 36 37 38 39 40 41 42 43
44 45
46 47 48 49 50 51 52 53 54 55 56 57 58
59 60
61 62
'''''''
'''''''
'''''''
''''''
[ RING ]
19 20 21 22 23 24 25 26 27 28 29 30
32 34 37 38 39 40 42 44
This is the ring I created plane in the index file.
I used this command line
g_dist -f PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 20000
-o DistPAP8HEP.xvg
but got the following like
I want to get the mean separation distance between two consecutive
polyaromatic rings along the axis of stacking
can someone help.
rob
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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