[gmx-users] g_order for all-atom simulations for double bonds
ramezanpour.mohsen at gmail.com
Fri Jan 12 06:22:02 CET 2018
Dear Gromacs users,
I have a bilayer composed of lipids with two unsaturated bonds in each tail.
I did my simulations in Gromacs v. 2016.3 in Charmm36FF.
BUT, I am doing the analysis in Gromacs v. 2016.2.
I want to calculate the order parameter for this lipid.
Here is what I do:
1) I calculate the S_cd for all the carbon atoms in each tail
2) I calculate the S_cd for two carbon atoms in the first double bond (with
3) I calculate the S_cd for two carbon atoms in the second double bond
(with -unsat option)
4) I replace the values from steps 2 and 3 in the output files from step 1.
This was the well-accepted approach for calculation of unsaturated tails
S_cd using g_order.
(please correct me if I am wrong)
Today, I came across a recent publication (I would recommend everyone to
look at) by Thomas Piggot et al. JCTC, 2017 which challenges this approach.
Briefly speaking, the standard g_order (even version 2016) seems to give
incorrect S_cd for double bonds.
The modified version of the g_order in this work seems to provide to give
much better values. However, it is recommended to be used when a UA force
field has been used for the simulation.
I was wondering what tools do you think I should use for this case, and why?
1) NMRlipids script for all_atom S_cd calculation
2) installing and using this modified version
3) if these modifications have been already implemented in the Gromacs
2016.3 or maybe newer versions if any.
Thanks in advance for your comments
*Rewards work better than punishment ...*
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