[gmx-users] Asymmetry in homo dimer simulation

[Erik Marklund]

5 dec 2012 kl. 17.26 skrev 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 :)
> 

I don't think that the use of single trajectories is necessarily "wrong", as long as they are sufficiently long. It's usually the amount of sampling that is the crucial point, no?

Erik

> -Justin
> 
> -- 
> ========================================
> 
> 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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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
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