Sorry to make this point here but running a 50ns simulation will take roughly 1 month on my system but a 10ns simulation will take 5 days on my system .. so would a 10ns be enough to monitor such motions .. also i request to u guide me to a link where I can find more about this independent simulation and how to run many replicates & analyze them ?? .....
On Wed, Feb 2, 2011 at 5:42 AM, Justin A. Lemkul <[email protected]> wrote: > > > bharat gupta wrote: > >> Sorry to ask this question but setting the gen_vel=yes and gen_seed = -1 >> will eventually lead to different simulation and thus different simulated >> structures ?? .. and after completing one set of simulation with this >> paramter and 3ns time .. do i have to repeat it some 3 or more times ??.... >> pls comment.. as I am going to start simulation with these parameters. >> >> > As I have already said, the combination of velocity generation with a > different random seed will give you (in theory) independent trajectories. > How many replicates you run is up to you. I certainly hope that, after all > I've said, you're still not intending on simply running 3-ns simulations, > regardless of how many replicates you run. If you're looking at loop > movements, you won't answer your questions with such little data. > > -Justin > > On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> bharat gupta wrote: >> >> Thanks for such a detailed reply to my queries .. But conducting >> a 50ns simulation will take time ... so i want to conduct >> independent simulation and for that I searched some threads but >> was not able to get the proper description and method... if u >> can guide me through an appropriate link .. it would be much >> more helpful .. >> >> >> Each simulation begins with the assignment of random velocities >> (gen_vel = yes). Specify different values of gen_seed (or leave it >> set to -1) to get different velocities each time. >> >> -Justin >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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 [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Bharat >> Ph.D. Candidate >> Room No. : 7202A, 2nd Floor >> Biomolecular Engineering Laboratory >> Division of Chemical Engineering and Polymer Science >> Pusan National University >> Busan -609735 >> South Korea >> Lab phone no. - +82-51-510-3680, +82-51-583-8343 >> Mobile no. - 010-5818-3680 >> E-mail : [email protected] <mailto:[email protected]> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : [email protected]
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