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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