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



--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php




--
========================================

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

========================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to