Hmm... Rotational time..? If you need diffusion constant, just use g_rotacf and then integrate the resulting VACF. If I recall correctly, you should make an index file with three numbers to define two vectors for the calculation.
On Wed, Sep 22, 2010 at 7:27 PM, Paymon Pirzadeh <ppirz...@ucalgary.ca> wrote: > Dear Dr. Chaban, > I meant the N-H bond vectors of protein backbone for calculation of > rotational time correlation function to calculate the rotational > diffusion constant of my protein. I need a protocol which walks me step > by step through the procedure. > Thanks for your Attention. > > Paymon > > > On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote: >> > Message: 2 >> > Date: Wed, 22 Sep 2010 12:07:27 -0600 >> > From: Paymon Pirzadeh <ppirz...@ucalgary.ca> >> > Subject: [gmx-users] rotational correlation function >> > To: gmx-users@gromacs.org >> > Message-ID: <1285178847.11669.66.ca...@paymon-desktop> >> > Content-Type: text/plain >> > >> > Hello, >> > Imagine if the total correlation function of a protein could be >> > factorized into rotational and internal portions: >> > Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t) >> > and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)? >> > What does the g_rms -fit do? I am confused on how I can use gromacs >> > commands on my output files. Sorry for mass of e-mails. >> > >> > Paymon >> >> >> Hey, Paymon - >> >> Do you mean the correlation function of the velocity (VACF)? Why not >> to use g_velacc and g_rotacf for translational and rotational VACFs? I >> suppose, your molecule is rigid (enough) for rotational velocoty to >> make sense. >> >> -- >> Dr. Vitaly V. Chaban >> Department of Chemistry >> University of Rochester >> Rochester, NY 14627-0216 >> United States of America > > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
