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
