OK, To summurize: 1. I calculate the Ctot(t) with g_rotacf using N-H index files.
2. Use trjconv to get a trajectory of internal motions. => How I get the Cint(t)??? 3. Crot = Ctot/Cint But, is there any way to calculate the Crot(t) directly? Is trjconv the solution again? regards, Paymon On Thu, 2010-09-23 at 20:40 +0200, David van der Spoel wrote: > On 2010-09-23 20.38, Paymon Pirzadeh wrote: > > Great tips and advices. I appreciate your attention. > > But, what would the g_rms -fit rot+trans do? > > compute the rmsd. something different. I said trjconv. > > > > 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 > > > > > -- > 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