thank justin > > > On 7/17/13 8:19 AM, pooja_gu...@nccs.res.in wrote: >> i took only single structure >>> > > You can't calculate entropy from a single structure. Please investigate > the > literature. > > -Justin > >>> >>> On 7/17/13 8:09 AM, pooja_gu...@nccs.res.in wrote: >>>> okk >>>> >>>> This may be very basic question. >>>> I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. >>>> I >>>> picked up one unfolded structure from the trj and solvated with water. >>>> I >>>> ran em for full system. now i am calculating the entropy. I afraid if >>>> i >>>> missed something. >>>> >>> >>> Are you running g_covar on the original 10 ns trajectory, or on a >>> single >>> energy-minimized structure? That latter would not make sense. >>> >>>> I am doing this first time. >>> >>> There is a large body of literature on configurational entropy related >>> to >>> the >>> quasiharmonic approximation. I would suggest you look into its >>> underlying >>> theory and how others apply it to biomolecular simulations. >>> >>> -Justin >>> >>>>> >>>>> On 7/17/13 7:56 AM, pooja_gu...@nccs.res.in wrote: >>>>>> I used system (0) for g-covar. >>>>>> >>>>> >>>>> Most likely, g_anaeig is running out of memory. Try using some >>>>> subset >>>>> of >>>>> the >>>>> system, like the protein only or its backbone. >>>>> >>>>> -Justin >>>>> >>>>>>> On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote: >>>>>>>> thanks for reply >>>>>>>> >>>>>>>> i am using Gromacs 4.5.5 version >>>>>>>> command >>>>>>>> g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d >>>>>>>> -comp >>>>>>>> >>>>>>> >>>>>>> What was the g_covar command used to generate the eigenvector .trr >>>>>>> file? >>>>>>> What >>>>>>> group did you choose for analysis during g_covar? >>>>>>> >>>>>>> -Justin >>>>>>> >>>>>>> -- >>>>>>> ================================================== >>>>>>> >>>>>>> Justin A. Lemkul, Ph.D. >>>>>>> Postdoctoral Fellow >>>>>>> >>>>>>> Department of Pharmaceutical Sciences >>>>>>> School of Pharmacy >>>>>>> Health Sciences Facility II, Room 601 >>>>>>> University of Maryland, Baltimore >>>>>>> 20 Penn St. >>>>>>> Baltimore, MD 21201 >>>>>>> >>>>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>>>> >>>>>>> ================================================== >>>>>>> -- >>>>>>> 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 >>>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> ================================================== >>>>> >>>>> Justin A. Lemkul, Ph.D. >>>>> Postdoctoral Fellow >>>>> >>>>> Department of Pharmaceutical Sciences >>>>> School of Pharmacy >>>>> Health Sciences Facility II, Room 601 >>>>> University of Maryland, Baltimore >>>>> 20 Penn St. >>>>> Baltimore, MD 21201 >>>>> >>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>> >>>>> ================================================== >>>>> -- >>>>> 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 >>>>> >>>> >>>> >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> ================================================== >>> -- >>> 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 >>> >> >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > 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 >
-- Pooja Gupta, Ph.D. DBT-RA, Lab of Structural Biology National Centre for Cell Science NCCS Complex,University of Pune Campus Ganeshkhind, Pune 411007 India Email: pooja_gu...@nccs.res.in/ poojagupta....@gmail.com Phone: +91-20-25708158 -- 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
