Sir, Thank you for your suggestions. I decided the cutoff based on RMSD convergence. I will calculate at different time intervals. Running multiple simulation is definitely the best suggestion but due to time and machine constraint it would be difficult. Instead I have two mesophilic simulations. But Is there any other way by which I can prove this point?
Thank you Kavya On Wed, Dec 5, 2012 at 9:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/5/12 11:13 AM, Kavyashree M 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). >> >> > I would suggest you compare different, overlapping blocks of time as a > further assessment of convergence. What motivated the choice of the 4-50 > ns time frame? Simple RMSD stability? While that may be one way to assess > convergence, it is not necessarily definitive. If you analyze your RMSF > results over different times, i.e. 4-50, 10-50, 20-50, etc, how do they > compare? > > > As you have mentioned I do not have replicates of simulations >> hence only one 50ns simulation per temperature. >> >> > I would encourage you to run more simulations. One trajectory is not > definitive. > > -Justin > > 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://vt.edu/Pages/Personal/justin> >>> <h**ttp://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> >>> <htt**p://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<h**ttp://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> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**========== > > 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? 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