<div><span style>Hello,</span></div><div><span style><br></span></div><span style>I simulated a pure DPPC bilayer at 323 K under semi-isotropic conditions and have a somewhat small area per lipid of .615 nm^2. I also wrote my own code to calculate the average Mean Square Displacement and Diffusion Coefficient of the lipids, taking into account the relative motions of the monolayers, and am getting a result of around 5.4 x 10^-8 cm^2/s for a box size of 256 lipids/leaflet and around 4 x 10^-8 cm^2/s for a box size of 64 lipids/leaflet. I am trying to compare my code directly to the built in GROMACS result for g_msd but am unsure how to properly remove the monolayer COM motions with g_msd. In the index file, I have a group of all the lipids in one leaflet and then use g_msd with the flags -rmcomm (so that I can remove the COM motion of a selected group) and -mol (so it calculates the MSD for the COM of each lipid in the leaflet):</span><div>
<span style><font color="#222222" face="arial, sans-serif"><br></font></span></div><div><span style><font color="#222222" face="arial, sans-serif"> g_msd -f md_0_1.xtc -s md_0_1.tpr -n diffusionIndex.ndx -o output -rmcomm -b 10000 -mol</font></span></div>
<div><span style><br></span></div><div><span style>I then choose this one leaflet grouping for "Select a group to calculate mean squared displacement for" and for "Now select a group for center of mass removal", thinking that this would calculate the MSD of each lipid with respect to the COM of the monolayer. It then says "Split group of 3200 atoms into 64 molecules", which seems correct, but then it freezes and does not calculate. Is this calculation just extremely slow? If you used g_msd for removing center of mass motion of the monolayers, could you please let me know what groupings/flags you used to properly calculate the MSD? Many publications also seem to have diffusion coefficients more along the lines of 10x10^-8 for DPPC bilayers at 323 K, so does being off by a factor of 2 still seem reasonable? I appreciate any help you can provide.</span>
</div><div><span style><br></span></div><div><span style>Thanks,</span></div><div><span style>David</span></div>