[gmx-users] g_rotacf to calculate order parameter S2
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jan 2 11:37:01 CET 2004
On Thu, 1 Jan 2004, Byungchan Kim wrote:
>I want to calculate S2 order parameter with g_rotacf.
>>From mailing list discussion, I could figure out how to use g_rotacf on my
>purpose. My command is like this,
>g_rotacf -f 4pti.trj.xtc -n NH_21.ndx -d -P 2
>NH_21.ndx is like this
>My problem is that I couldn't get the flat value of correlation function.
>The simulation lasted up to 1.5 ns.
>What I am curious about is whether the program use orientation of
>interatomic vector "in molecular frame". Actually, I am not sure it is a
>problem if the program does not use the molecular frame.
>I am looking forward to hearing clever answer.
g_rotacf does not use the moleuclar frame. You can try to run the
trajectory through trjconv first, fitting everyhting to reference
structure (and only outputting the protein) and then run g_rotacf.
>Thank you very much and Happy New Year.
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users