[gmx-users] order parameters of partially unsaturated chains
Ángel Piñeiro
angel.pineiro at usc.es
Mon Jan 10 15:13:37 CET 2011
Thank you very much Javier. I think it is just a matter of convention
but I also think the convention is not clear since not everybody does
the same and so it is difficult to compare to what has already been
published. I think most of the papers do not use the convention for
unsaturated or partially unsaturated chains since this is not usually
mentioned...
Best wishes,
Ángel.
On Mon, 2011-01-10 at 14:16 +0100, JAVIER CEREZO BASTIDA wrote:
> Hello Angel.
>
> I found a detailed description of the order parameter conventions to
> describe molecular axis in a paper from Heller et al (JPC, 97,
> 8343-8360), including the case of unsaturated carbons. It should be
> equivalent to the implementation in GROMAS.
>
> In practice, I don't know the best way to do it, but your proposal
> sounds reasonable.
>
> Javier
>
> Ángel Piñeiro <angel.pineiro at usc.es> escribió:
>
> > Dear all
> > I wonder which is the best way to determine the deuterium order
> > parameters of partially unsaturated chains like the oleoyl chain of
> > POPC, more specifically I wonder if I should use the -unsat flag in
> > g_order for this case. I checked several papers on unsaturated lipids,
> > see for instance:
> > 1.- http://persweb.wabash.edu/facstaff/FELLERS/publications/jpc_01.pdf
> > 2.-
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1225825/pdf/biophysj00084-0102.pdf
> > 3.-
> > http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B94RW-4V8X9MG-P-1&_cdi=56421&_user=10&_pii=S0006349597782596&_coverDate=11%2F30%2F1997&_sk=%23TOC%2356421%231997%23999269994%23800076%23FLP%23display%23Volume_73,_Issue_5,_Pages_2249-2849_%28November_1997%29%23tagged%23Volume%23first%3D73%23Issue%23first%3D5%23date%23%28November_1997%29%23&view=c&_gw=y&wchp=dGLbVlz-zSkzV&md5=778ad27c9fc1e0b3874b178e36451cb4&ie=/sdarticle.pdf
> > 4.- http://pubs.acs.org/doi/abs/10.1021/ja903529f
> > 5.- http://www.ibpc.fr/UMR7099/pdf/Warschawski05-1.pdf
> >
> > but it seems that nobody mentions anything about a correction for the
> > unsaturated carbons. Then I went to the code, I think this is the
> > important part:
> >
> > if (bUnsat) {
> > /* Using convention for unsaturated carbons */
> > /* first get Sz, the vector from Cn to Cn+1 */
> > rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i]+j]], dist);
> > length = norm(dist);
> > check_length(length, a[index[i]+j], a[index[i+1]+j]);
> > svmul(1/length, dist, Sz);-
> >
> > /* this is actually the cosine of the angle between the double bond
> > and axis, because Sz is normalized and the two other components of
> > the axis on the bilayer are zero */
> > sdbangle += acos(Sz[axis]);
> > } else {
> > /* get vector dist(Cn-1,Cn+1) for tail atoms */
> > rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i-1]+j]], dist);
> > length = norm(dist); /* determine distance between two atoms */
> > check_length(length, a[index[i-1]+j], a[index[i+1]+j]);
> >
> > svmul(1/length, dist, Sz);
> > /* Sz is now the molecular axis Sz, normalized and all that */
> > }
> >
> > As far as I see the difference is that by using the -unsat option, the
> > atoms Cn, Cn+1 are used to measure theta instead of the atoms Cn-1, Cn
> > +1. I think this could be reasonable when the whole chain is unsaturated
> > but I am not sure that it is correct to use the -unsat option when we
> > have two unsat carbons in the middle of a larger chain.... The
> > calculation could also be done for the whole chain without the -unsat
> > option, then repeat it for the unsaturated carbons plus their first
> > neighbors with the -unsat option and then replace the results obtained
> > from the second calculation for the central carbons in the curve
> > obtained without the -unsat option... as previously suggested in this
> > list (see
> > http://lists.gromacs.org/pipermail/gmx-users/2010-February/049072.html)
> > but I am not sure that is the best... I would appreciate any comment.
> >
> > Cheers,
> >
> > Ángel.
> >
>
>
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