[gmx-users] Asymmetry in homo dimer simulation
jalemkul at vt.edu
Thu Dec 6 14:47:17 CET 2012
On 12/6/12 5:26 AM, Erik Marklund wrote:
> 5 dec 2012 kl. 17.26 skrev Justin Lemkul:
>> On 12/5/12 11:21 AM, Kavyashree M wrote:
>>> 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?
Well, long simulations have issues too -
That said, there's probably not one single answer here. I am generally leery of
anyone trying to make arguments based on a single trajectory, especially one
that is relatively short by modern standards. Indeed, the simulation needs to
be sufficiently long to potentially observe the phenomenon of interest, and that
simulation should be converged and of adequate length to collect reasonable
statistics. I think, from a practical standpoint, several simulations of
intermediate length will give you better insight than a single simulation of any
length. Certainly in my work on amyloid peptides, multiple trajectories of
considerable length are prerequisite; most other papers get (rightly) thrown out
immediately. In the case of well-folded proteins whose behavior is more
predictable, you can probably get more information from a single high-quality
In the present case, where a simulation of modest length is not agreeing with
(presumably) experimental data, I think sampling or convergence is a major
concern. Had the trajectory reproduced the expected behavior, it's less of an
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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