[gmx-users] Trouble calculating MSD after removing COM for upper and lower leaflets

Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower

Re: [gmx-users] Trouble calculating MSD after removing COM for upper and lower leaflets

On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the

Re: [gmx-users] Trouble calculating MSD after removing COM for upper and lower leaflets

Hi Justin, 1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking at anisotropy in dynamics if any) 2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system (192/leaflet) If you were to remove the COM motion of individual leaflets and extract the MSD, what would

Re: [gmx-users] Trouble calculating MSD after removing COM for upper and lower leaflets

On 11/9/13 11:37 AM, rajat desikan wrote: Hi Justin, 1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking at anisotropy in dynamics if any) 2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system (192/leaflet) If you were to remove the COM motion of

Re: [gmx-users] Trouble calculating MSD after removing COM for upper and lower leaflets

Hi Justin, Thanks for your time. I think I will use g_traj to spit out the P8 coordinates from upperP8_center_pbcnojump.xtc and write my own little MSD routine :) On Sat, Nov 9, 2013 at 11:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 11:37 AM, rajat desikan wrote: Hi Justin, 1)