[gmx-users] Re: change in secondary structure
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 2 14:54:07 CET 2011
bharat gupta wrote:
> 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
A month is a reasonable time investment for quality MD simulations.
> my system .. so would a 10ns be enough to monitor such motions .. also i
Very doubtful, but I'm not going to speculate further. You have to be willing
to put in significant effort to answer complex questions, unless you're happy to
settle for potentially unreliable data.
> 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 ??
There's nothing left to say. I've told you how to initiate independent
simulations. Analyzing them is up to you based on your plans for this project.
No one on this list is going to provide you broad-reaching how-to's for doing
anything you might come up with. The manual is extensive, and the website/wiki
has lots of tips and information.
-Justin
> .....
>
> On Wed, Feb 2, 2011 at 5:42 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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.
>
> -Justin
>
> On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto: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> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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> --
> 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>
> <mailto: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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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>
>
> --
> 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
========================================
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