[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:

>Hi Folks.
>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
>329     333
>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.
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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

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