From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Sat Nov 10 2007 - 07:43:09 CST
Your model IS constructed based on experimental data, and during your calculation, it changes. So, you fix it to meet "experimental results", which is what the reviewers want. That's fudging, in my book.
I've also mentioned previously my concern about changing ensembles after equilibration. Perhaps that is why the volume changes on going from NVT to NPT, again to please reviewers. I was just at a CHARMM tutorial where we were told to "never simulate using NVT because experiments are always at 1 atm". I think changing horses in mid-stream leads to problems, but that is my opinion, I guess. I would also guess that the constant P piston is what is causing the membrane to compress.
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959
----- Original Message ----
From: Himanshu Khandelia <hkhandel_at_memphys.sdu.dk>
To: Richard Wood <rwoodphd_at_yahoo.com>
Sent: Saturday, November 10, 2007 3:20:47 AM
Subject: Re: namd-l: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield
No, this is not fudging results. This is modeling and simulation, and
model is constructed based on experimental data.
> > Isn't this just "fudging" results? It appears to me that you're
> > changing your results so they fit experimental ones by using one
> > equilibrate, and then another to do your production run. I thought
> > 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
> that one does for the production run, as I would think this would be
> thing that reviewers would be more concerned about than one's area
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
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
> would be close to the "correct size".
Good idea, but the area per lipid does not shrink during equilibration,
keeps shrinking during equilibrium dynamics. A variation of what you
suggested has been mentioned in the list before. Check this out:
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