[gmx-users] Re: change in secondary structure

[bharat gupta]

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.
>
> -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
>>
>>    ========================================
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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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-- 
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
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