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.pine...@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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