[gmx-users] Re: change in secondary structure

Wed Feb 2 15:01:24 CET 2011

Anyways thanks for ur detailed answers .. After completing the simulation ,
the 10ns one I will get back to u if any doubt arises .. Also I am running a
3ns simulation of the same variant of GFP but with a different FF ... hoping
to get any positive result for that one ...

On Wed, Feb 2, 2011 at 5:54 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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-- 
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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