From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Sat Nov 10 2007 - 02:20:47 CST
No, this is not fudging results. This is modeling and simulation, and any
model is constructed based on experimental data.
> > Isn't this just "fudging" results? It appears to me that you're just
> > changing your results so they fit experimental ones by using one method to
> > equilibrate, and then another to do your production run. I thought science
> > was about learning new things, and not "pleasing" reviewers.
Its not about pleasing reviewers. Its about doing it the best method
currently available. (Un)fortunately, often in science, there is no
consensus about one single best method.
> I would think one would want to do equilibration using the same method
> that one does for the production run, as I would think this would be one
> thing that reviewers would be more concerned about than one's area per
Why should one equilibrate and run dynamics using the same ensemble ?
Equilibration is only to obtain a local energy minimum, so that the
simulation is stable during equilibrium sampling. As long as one is doing
equilibrium sampling in a single thermodynamic ensemble in the phase
space, who cares how the equilibration was done ?
> I would also think that if the area per lipid shrinks, one could
> start with a larger lipid so that when it shrinks during equilibration, it
> would be close to the "correct size".
Good idea, but the area per lipid does not shrink during equilibration, it
keeps shrinking during equilibrium dynamics. A variation of what you have
suggested has been mentioned in the list before. Check this out:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6861.html
-Himanshu
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