[gmx-users] g_order for all-atom simulations for double bonds
T.Piggot at soton.ac.uk
Fri Jan 12 13:15:07 CET 2018
Regarding g_order/gmx order being incorrect for unsaturated carbons, there is a bug about this (https://redmine.gromacs.org/issues/1166). I would say that I would fix it, but my C/C++ coding isn't good enough to be able to do this properly. Perhaps a warning could/should be issued by the program about this problem until it is fixed?
Anyway, even if it wasn't incorrect, it is designed to work on united-atom systems for the carbon-deuterium order parameter calculation. So the program effectively predicts the positions of the hydrogen atoms and uses these predictions in the calculation. If you already have the hydrogen atoms there (as in your all-atom simulations) it doesn't make sense to start by first ignoring them and second then trying to predict where they might. Rather using the actual hydrogen atom positions in the calculation will give you the most accurate results.
As for the tool to use in the all-atom calculation, it doesn't really matter as long as it works using the actual hydrogen atom positions. The NMRlipids script is one, lots of others are mentioned or referenced in the paper and you can even make your own pretty easily should you wish to do so (e.g. I've made one with python/MDAnalysis in the past). One thing to look out for is that some tools will automatically average the order parameters for hydrogens attached to the same carbon which you may not want.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mohsen Ramezanpour [ramezanpour.mohsen at gmail.com]
Sent: 12 January 2018 05:21
To: Discussion list for GROMACS users; Discussion list for GROMACS users
Subject: [gmx-users] g_order for all-atom simulations for double bonds
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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