minnale wrote:
Hi all,
I am trying to make centre of the bilayer so I used following command line
trjconv -f 20nspopc.xtc -centre rect -o 20nstrjout.xtc -n water.ndx
based on http://www.gromacs.org/pipermail/gmx-users/2003-June/005995.html
here I selected 3 (solution) again 3 (solution) for output of the
selecting group
this command ran fine
when I feed 20nstrjout.xtc to g_density
g_density -f 20nstrjout.xtc -s em.tpr -d z -o waterden -n water.ndx
Group 0 ( System) has 14036 elements
Group 1 ( POPC) has 6656 elements
Group 2 ( SOL) has 7380 elements
Group 3 ( SOL) has 7380 elements
Select a group: 3
Selected 3: 'SOL'
Reading frame 0 time 0.000 Segmentation fault
where is the mistake happening?
SOL is not "solution," it is "solvent," i.e. water. If you want to center
around the water, with the bilayer leaflets on opposite sides of the box, that's
what you'll get. If you want to center about POPC, then select POPC.
-Justin
Could anyone tell me
Thanks in advance
ICL
<http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2657076_2649302/2660191/1?PARTNER=3&OAS_QUERY=null>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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 [email protected]
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
