Great tips and advices. I appreciate your attention. But, what would the g_rms -fit rot+trans do?
Paymon On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote: > On 2010-09-23 18.14, Paymon Pirzadeh wrote: > > Dear Dr. van der Spoel, > > Thanks a lot for your clarification. But some questions yet: > > > > 1. If I do not provide the "-aver" option, will the program calculate > > the C(t) for individual N-H bond? > > > Yes. > > > 2. In a paper that I just read, JCP vol. 131 155103 (2009), they claim > > they have calculated the Ctot(t) which could be factorized into > > rotational and internal components, Ctot(t)=Crot(t)*Cint(t). I assume > > g_rotacf gives the rotational part. How one can calculate the Ctot(t) > > (they claim they calculatetd the Ctot and Crot with GROMACS utilities)? > > How can we generate the rotation matrix (omega(t)) and use it? What's > > the use of "-fitfn"? Is it sth that could be done in other data > > processing softwares? > If your sim is long enough (10-20 times the rotation time, which for a > small protein is on the order of a couple of ns) you can fit all the > individual NH -acfs to two exponentials, 1 for the NH relaxation and one > for the overall. > > > > > 3. How can we generate a trajectory with no internal motions? Does it > > have anything to do with g_rms? > You can do the reverse by fitting trjconv -fit rot+trans this will give > you a protein with no overall rotation+translation from which you can > derive the order parameters and relaxation times of individual NH vectors. > > > Check this ref too: > @Article{Villa2006a, > author = {A. Villa and G. Stock}, > title = {What NMR relaxation can tell us about the internal motion > of an RNA > hairpin: A molecular dynamics simulation study}, > journal = {J. Chem. Theory Comput.}, > volume = {2}, > year = {2006}, > pages = {1228-1236}, > } > > > > > Sorry for mass of questions. > > Regards, > > > > Paymon > > > > > > On Thu, 2010-09-23 at 08:20 +0200, David van der Spoel wrote: > >> On 2010-09-23 01.27, Paymon Pirzadeh 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. > >> define all NH bonds in an index file as > >> [ NH ] > >> 5 6 > >> 10 11 > >> 23 24 > >> > >> etc. > >> > >> Then run g_rotacf -P 2 [ more flags ] -aver > >> Analyze the ACF to extract the order parameters. > >> You will need to read Lipari& Szabo papers: > >> @Article{ Lipari82a, > >> author = "G. Lipari and A. Szabo and R. M. Levy", > >> title = "Protein Dynamics and {NMR} relaxation: comparison of > >> simulations with experiment", > >> journal = BTnature, > >> year = 1982, > >> volume = 300, > >> pages = "197-198" > >> } > >> > >> @Article{ Lipari82b, > >> author = "G. Lipari and A. Szabo", > >> title = "Model-Free Approach to the Interpretation of Nuclear > >> Magnetic Resonance Relaxation in > >> Macromolecules. 1. Theory and Range of Validity", > >> journal = BTjacs, > >> year = 1982, > >> volume = 104, > >> pages = "4546-4559" > >> } > >> > >> > >>> > >>> 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 > >>> > >> > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Dept. of Cell& Molec. Biol., Uppsala University. > >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > >> sp...@xray.bmc.uu.se http://folding.bmc.uu.se > > > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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