Thielges, Sabine wrote:
Hi,
I have done a MD of a system GPCR/POPC, and I was trying to check my membrane with g_order. I made the index file like indicated in the web site using
make_ndx -f md_0_10.tpr -o sn1.ndx
12 & a C15 | a C14 | a C6 | a C1 | a C2 | a C3 | a C5 | a C7 | a C4 | a C5 | a
C7 | a C4 | a C8 | a C9 | a C10 | a C11 | a C12 | a C13 |
Each carbon atom must be considered in separate groups. See, for example:
http://oldwiki.gromacs.org/index.php/g_order
<snip>
There no number. It is like nothing happen. I didn't had that issu for the rmsd
calculation or even density. I have a nice plot for both
Because the index group is wrong. See the above link and try again.
-Justin
Could somebody help me on that?
thank you in advance
Sabine
Dr. THIELGES Sabine
Associate Research Officer
Conseil national de recherches du Canada - National Research Council
Institut de recherche en biotechnologie - Biotechnology Research Institute
6100, avenue Royalmount, Montréal, Québec, H4P 2R2
tél: (514) 496-6255
[email protected]
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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