[gmx-users] Re: change in secondary structure

[Justin A. Lemkul]

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 <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
> 
> 
>     -- 
>     ========================================
> 
>     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    gmx-users at gromacs.org
>     <mailto:gmx-users at 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-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     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 : 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================