GROMACS version: 2020.2
GROMACS modification: No
I have a problem. I tested new parameters for POPC. With old parameters, everything is ok probably.
My molecular order parameter - model with old parameters
My molecular order parameter - model with new parameters
Is it possible that the order parameter is higher for the segments which are further from the headgroup of lipidis? Maybe parameters are wrong
I made an index file for C atoms in the oleoyl acyl chain
there was no error
And then I computed order parameters for my oleyol chain
for all segments
gmx order -s eq2.tpr -f eq2.xtc -n sn1.ndx -nr sn1.ndx -d z -od deuter_sn1.xvg -b 200000 -e 300000
And only for 9-10 segment ( double bond)
gmx order -s eq2.tpr -f eq2.xtc -n unsat_sn1.ndx -nr unsat_sn1.ndx -d z -od deuter_sn1_unsat.xvg -unsat -b 200000 -e 300000
I have also another question. How can I read values of order parameters from NMR (I want to compare experimental values to values from my models)?
Here I have only line graph in figure 3 https://pubs.rsc.org/en/content/articlehtml/2013/cp/c2cp42738a
But I need a value like in gromacs:
Maybe I should estimate values from the graph or write to authors and they will give me accurate results?
Thanks in advance.
First things first, which force field are you using? If it is an all-atom force field, you shouldn’t really use gmx order. In addition, the gmx order -unsat option doesn’t work correctly and should not be used. See https://pubs.acs.org/doi/10.1021/acs.jctc.7b00643 for lots of information on these points.
With regards to your plot, it looks almost certainly like you’ve got the ordering of your index groups wrong (tail to head perhaps?). Please double check what you are doing.
For the experimental data from that paper (including the C2 splitting):
2.00000000 -0.0795825 -0.122519
3.00000000 -0.180265 nan
4.00000000 -0.186187 nan
5.00000000 -0.193592 nan
6.00000000 -0.166198 nan
7.00000000 -0.154356 nan
8.00000000 -0.1203 nan
9.00000000 -0.108455 nan
10.00000000 -0.0225792 nan
11.00000000 -0.0581141 nan
12.00000000 -0.0995716 nan
13.00000000 -0.106234 nan
14.00000000 -0.0943887 nan
15.00000000 -0.0943887 nan
16.00000000 -0.0899483 nan
17.00000000 -0.0669979 nan
18.00000000 -0.0181358 nan
Thank you so much. I will check. I use the OPLS-AA force field. These new parameters are not so good. My colleagues who prepared parameters focus mostly on new torsional angle parameters and charges for the head group without considering acyl chains (include double bonds). I used the same index file for both these models (because the structure is the same 200 POPC molecules, 6000 SOL), so it should be ok, but it is better to check. I will prepare the paper, so yes I think that I will compute that again with a program from your paper.
Do you have also experimental data from that paper Cholesterol and POPC segmental order parameters in lipid membranes: solid state 1H–13C NMR and MD simulation studies - Physical Chemistry Chemical Physics (RSC Publishing) for palmitoyl chain?
For palmitoyl my order parameters looks much better.
Model with new parameters
But also I will try to use your program
The data for the palmitoyl chain is:
As you are using an all-atom force field, I’d strongly recommend using something other than gmx order (either the standard one or the modified one in my paper). It really doesn’t make any sense to ignore the hydrogen atoms but then try to guess where they are (which is what gmx order and other united-atom analysis methods do).
I should say that this is (obviously) -Scd for the sn-1 experimental data.
And it’s almost certain that something is incorrect in your analysis with your new parameters but I can’t say more than that without seeing the files.
I’ve had a quick look and your index file seems fine (well apart from it being named sn-1 but is for the sn-2 tail!). I’ve also calculated the order parameters using gmx order on the final frame give similar results to the ones you shared despite far less data to average over.
So in contrast to what I said before, I think you’re probably right in that the parameters are to blame (well apart from the order parameters at the double bond that need calculated using something other than gmx order; as I said, ideally you should use an all-atom method) but I can’t be completely certain from just a quick look. I haven’t got the time to examine the parameters and see what has been modified but something fairly major is changing in the ordering of the tails. I suggest either using the older parameters or going through the modifications one by one to see what is causing the changes. Or you could always use a completely different force field.
Sorry I can’t be of more help.
You have already helped me a lot. I’d like to thank you for everything, I owe you one. I will try to find new solution.