![]() Gmx density -s md_0_1.tpr -f md_0_1.xtc -n density_groups.ndx -o dens_headgroups.xvg -d Z Now analyze each of these groups separately (note that Protein and SOL are already included in the index file) using the density module: Gmx make_ndx -f md_0_1.tpr -o density_groups.ndx An index group for the lipid headgroups and acyl chains of DPPC can be created by entering the following: The latter two groups are standard, and do not require any special manipulation. One generally sees analysis of membrane density broken down into several different groups - lipid headgroups, acyl chains (sometimes broken down even further to glycerol, methylene, and terminal methyl groups), protein, and solvent. As such, there are no values for carbon 1 (ester carbon) or 16 (terminal methyl) in each palmitoyl chain. The plot above was rendered after re-numbering the output file from 2, reflecting the fact that we have analyzed all applicable carbon atoms in each chain. The order program does not know which segment of the acyl chain has been chosen, so it simply numbers the output from 1. It is not possible to compute -S CD for terminal carbon atoms, as they lack neighboring atoms from which the local molecular axis is computed. Note that the order program, by default, numbers the carbon atoms in each chain from 1. ![]() ![]() The result of the calculation will look something like this: Gmx order -s md_0_1.tpr -f md_0_1.xtc -n sn1.ndx -d z -od deuter_sn1.xvgĭeuterium order parameters can be helpful in verifying whether or not your membrane entered a gel phase during the simulation. To calculate deuterium order parameters with the normal to the bilayer along the z-axis, use the GROMACS order module: This process should then be repeated for the sn-2 chain (carbons C15, C17-C31 to give "sn2.ndx"). We then deleted all the unnecessary groups (del 0-21). What we have just done is create an index group for the sn-1 chain of DPPC by matching all the atoms in one chain of the lipid with specific atoms names of carbons in the acyl chain. Each chain must be considered separately! Most of these analyses will require the use of specialized index groups, generated by make_ndx.įor deuterium order parameter analysis, you will need an index group that contains only the carbons along the lipid acyl chains. Other analyses should be considered, such as secondary structure of the peptide, RMSD, P-N vector orientation, helix tilt, etc. Deuterium order parameters of the acyl chains.Several parameters that may be of interest: There are several types of analyses that are particularly useful for membrane protein systems.
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