[gmx-users] Asymmetry in homo dimer simulation

[Kavyashree M]

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.

Thank you
Kavya


On Thu, Dec 6, 2012 at 3:56 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

>
> 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
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
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