[gmx-users] Asymmetry in homo dimer simulation

[Justin Lemkul]

On 12/6/12 5:46 AM, Kavyashree M wrote:
> Sir,
>
> I also have come across several papers where they have done
> single simulations but in recent days most of them perform
> multiple trajectories for shorter period. But I am not clear how
> can multiple trajectories for shorter period of time compensate
> for single extended time simulation.
>

See my previous post.  Several trajectories, starting from independent 
conditions (at least random velocities if not different configurations) lead to 
much better sampling, and if they converge to reinforce the argument you are 
making, the case is vastly stronger than if one simulation happens to produce 
some interesting result.  Just because you can do something once doesn't 
necessarily make it true :)

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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