[gmx-users] Re: change in secondary structure
bharat.85.monu at gmail.com
Wed Feb 2 14:50:10 CET 2011
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 <jalemkul at vt.edu> 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.
> On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> 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 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
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> 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-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 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 : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
> 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
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users