[gmx-users] doubt in deuterium order parameter

Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the angle between the bilayer normal and the

[gmx-users] order parameter

Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the angle between the bilayer normal and the –C

RE: [gmx-users] order parameter

Hi, Thanks lot for replying. I am doing all-atom simulation. I am doing the PBC before finding the angle. also I normalise the vectors before finding the angle. Yes I have checked that the formula I am using for the order parameter is correct. I am doing the averaging correctly. 1. I take

RE: [gmx-users] order parameter

[X] Hi Justin, Thanks for the reply, and this is the graph, the red curve is what GROMACS gives, the blue curve is what I get.. yes I am considering the unsaturated carbons in to account. I have to see which is closer to the experimental result. Hi Chris, Thanks for the information , I will s

[gmx-users] Deuterium order parametr

Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the angle between the bilayer normal and the -C

RE: [gmx-users] Deuterium order parametr

list for GROMACS users Subject: Re: [gmx-users] Deuterium order parametr Parthasarathi, Ramya wrote: > Hi, > > > > I am trying to write a code for Deuterium order parameter of DOPC lipid. > I went through the code in gmx_order.c, I did the following, > > > &g