[gmx-users] order parameters of partially unsaturated chains

Ángel Piñeiro angel.pineiro at usc.es
Sat Jan 8 10:25:30 CET 2011

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
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
but I am not sure that is the best... I would appreciate any comment.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110108/491d5c2d/attachment.html>

More information about the gromacs.org_gmx-users mailing list