thanks for your reply i have got output file,i used the following options: # g_order -f md.xtc -s md.tpr -n sn1.ndx -o order-sn1.xvg -od deuter-sn1.xvg -d z
whatever deuter-sn1.xvg get me is the same Sc-c (the vector Ci-1,Ci,Ci+1 is considered as molecule vector)? where i used the united atoms force field for my system. thanks very much, Afsaneh On Sun, Feb 7, 2010 at 7:14 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > afsaneh maleki wrote: > >> Hi all, >> >> i used united the atom force field model for the membrane lipids . to >> calculate order parameter i used : >> g_order -od -d >> i know united atom force field doesn't have hydrogen atoms in >> hydrocarbons chains . >> i want to know gromacs calculates order parameter * Sc-c* or *Sc-d* >> (Deuterium) ? >> > > Simple geometry. > > > >> in the output is written: title "Deuterium order parameters" >> >> > Is that it? If you've got an empty output, then your index file probably > wasn't prepared correctly. There is a how-to on the g_order page on the > Gromacs website: > > http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order > > -Justin > > thanks in advance, >> Afsaneh >> >> > -- > ======================================== > > 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 > -
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