[gmx-users] Re: change in secondary structure
bharat.85.monu at gmail.com
Wed Feb 2 14:39:06 CET 2011
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.
On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul <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
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> ICTAS Doctoral Scholar
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> Department of Biochemistry
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