Dear users, One more question is. Is there a way to prove my point?
Thank you Kavya On Wed, Dec 5, 2012 at 9:43 PM, Kavyashree M <hmkv...@gmail.com> wrote: > Sir, > > Thank you for the reply. Total simulated time is 50ns. > first 4ns is left and only 4-50ns were considered for > rmsf calculations. T1 is 300K and T2 is 363K the protein > being simulated is from Ecoli (mesophilic). > > As you have mentioned I do not have replicates of simulations > hence only one 50ns simulation per temperature. > > And this happened in two proteins that I had simulated both > are form mesophilic origin. > > Thank you > Kavya > > On Wed, Dec 5, 2012 at 9:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 12/5/12 10:56 AM, Kavyashree M wrote: >> >>> Dear users, >>> >>> I have simulated a homodimer (both the chains with same number >>> of amino acids and in same configuration) using gromacs 453 in >>> OPLSAA force field at 2 different temperatures (say T1 and T2). It >>> was noticed that the rms fluctuation of chain A differs from chain B >>> in both the simulations. In one of the temperature (T2) the rmsf of the >>> protein is supposed to be more compared to the other (T1). >>> >>> When I compare rmsf of chain A at T1 with chain A at T2 (similarly for >>> chain B). I observed that it shows opposite behaviour. ie chainB is >>> having increased fluctuation at T1 than at T2. >>> >>> But actually i observed that the fluctuation of chain A at T1 resembles >>> the fluctuation of chain B at T2 (with increased values) and similarly >>> the fluctuations of chain B at T1 resembles that of chain A fluctuation >>> at T2 (with increased values). >>> >>> Is this possible? or is there anything wrong? >>> >>> >> Your results would indicate simply that while one protein subunit >> fluctuates more, the other becomes somewhat more rigid. That's plausible, >> but perhaps not intuitive. Keep in mind that RMSF is very sensitive to >> whether or not your simulations are actually converged, and a single >> trajectory under each condition is insufficient to make very solid claims >> about anything. How long are the simulations? How much of the initial >> time is being disregarded, and thus how long are the equilibrated segments >> of the simulations? How different are T1 and T2? >> >> -Justin >> >> -- >> ==============================**========== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> ==============================**========== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- 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
