[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

I have patched g_order version 4.5.4 to compute the order parameters in a different way. Despite trying, I don't understand the original g_order implementation. In the version that I am providing, the hydrogens are explicitly built and the coordinates of these hydrogens are output to

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Hi Igor, Thanks for the reply but I think you slightly missed the point I was trying to make. I followed the approach you mention for the double bond and (with the two force fields I tried) got the values I discussed in my last email, which when compared to the published values seem to be

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Hi, Both the trajectories are 100 ns in length (plus I have a repeat of each simulation using different starting velocities). The results from a block analysis, and analysis of the repeat simulations, give almost identical results to those in my previous message. The other thing is that the

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Further to my last message we have managed to use a tcl script in VMD to calculate the order parameters for the POPC chains in the CHARMM36 simulation. I have put the values for this calculation and the values I obtained using g_order (over the same period in the same trajectory) below (this

[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Dear Thomas: I agree with your conclusions about g_order. My usage of the Berger POPC lipids in combination with the g_order command (as per the instructions in http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order ) yields order parameters of 0.193 and 0.051 for the first and

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

chris.ne...@utoronto.ca wrote: Dear Thomas: I agree with your conclusions about g_order. My usage of the Berger POPC lipids in combination with the g_order command (as per the instructions in http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order ) yields order parameters of 0.193

[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Hi Everyone, I am facing a problem when calculating the lipid deuterium order parameters for the unsaturated carbons of the sn-2 tail of POPC using g_order with GROMACS version 4.5.4 (although I have tried other older versions too but they all give the same results). Firstly, I should say

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

thomas, i've recently placed a similar question and justin asked me to show my index for the double bound calculation, so, i'm asking you the same. you should have Ci-1 Ci - the first carbon of the double bound Ci+1 - the second carbon of the double bound Ci+2 in that index doing this,