Sir, I also have come across several papers where they have done single simulations but in recent days most of them perform multiple trajectories for shorter period. But I am not clear how can multiple trajectories for shorter period of time compensate for single extended time simulation.
Thank you Kavya On Thu, Dec 6, 2012 at 3:56 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > > 5 dec 2012 kl. 17.26 skrev Justin Lemkul: > > > > > > > On 12/5/12 11:21 AM, Kavyashree M wrote: > >> 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? > >> > > > > Not using single trajectories. Your job is to convince reviewers that > your work is sound. A single trajectory is not convincing, at least to any > reviewer that does his or her homework :) > > > > I don't think that the use of single trajectories is necessarily "wrong", > as long as they are sufficiently long. It's usually the amount of sampling > that is the crucial point, no? > > Erik > > > -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 > > > > ======================================== > > -- > > 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 > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > 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 > -- 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
