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Dear all<BR>
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:<BR>
1.- <A HREF="http://persweb.wabash.edu/facstaff/FELLERS/publications/jpc_01.pdf">http://persweb.wabash.edu/facstaff/FELLERS/publications/jpc_01.pdf</A><BR>
2.- <A HREF="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1225825/pdf/biophysj00084-0102.pdf">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1225825/pdf/biophysj00084-0102.pdf</A><BR>
3.- <A HREF="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">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</A><BR>
4.- <A HREF="http://pubs.acs.org/doi/abs/10.1021/ja903529f">http://pubs.acs.org/doi/abs/10.1021/ja903529f</A><BR>
5.- <A HREF="http://www.ibpc.fr/UMR7099/pdf/Warschawski05-1.pdf">http://www.ibpc.fr/UMR7099/pdf/Warschawski05-1.pdf</A><BR>
<BR>
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:<BR>
<BR>
if (bUnsat) {<BR>
/* Using convention for unsaturated carbons */<BR>
/* first get Sz, the vector from Cn to Cn+1 */<BR>
rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i]+j]], dist); <BR>
length = norm(dist);<BR>
check_length(length, a[index[i]+j], a[index[i+1]+j]);<BR>
svmul(1/length, dist, Sz);<BR>
<BR>
/* this is actually the cosine of the angle between the double bond<BR>
and axis, because Sz is normalized and the two other components of<BR>
the axis on the bilayer are zero */<BR>
sdbangle += acos(Sz[axis]); <BR>
} else {<BR>
/* get vector dist(Cn-1,Cn+1) for tail atoms */<BR>
rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i-1]+j]], dist);<BR>
length = norm(dist); /* determine distance between two atoms */<BR>
check_length(length, a[index[i-1]+j], a[index[i+1]+j]);<BR>
<BR>
svmul(1/length, dist, Sz);<BR>
/* Sz is now the molecular axis Sz, normalized and all that */<BR>
}<BR>
<BR>
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.<BR>
<BR>
Cheers,<BR>
<BR>
Ángel.
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