[gmx-users] Asymmetry in homo dimer simulation

[Justin Lemkul]

On 12/5/12 11:21 AM, Kavyashree M wrote:
> Sir,
>
> Thank you for your suggestions. I decided the cutoff based on
> RMSD convergence. I will calculate at different time intervals.
> Running multiple simulation is definitely the best suggestion but
> due to time and machine constraint it would be difficult. Instead
> I have two mesophilic simulations. But Is there any other way
> by which I can prove this point?
>

Not using single trajectories.  Your job is to convince reviewers that your work 
is sound.  A single trajectory is not convincing, at least to any reviewer that 
does his or her homework :)

-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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