Re: [gmx-users] g_msd and pbc

Thanks Tsjerk for the information. It would be very nice if you can elaborate it. I am unable to understand. -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Dec 8, 2011 at 12:10 AM, Tsjerk Wassenaar wrote: > Hi Chandan, > > Pretty simple; you just take the smallest distance between the time

Re: [gmx-users] g_msd and pbc

Hi Chandan, Pretty simple; you just take the smallest distance between the time points in the periodic system. Cheers, Tsjerk On Wed, Dec 7, 2011 at 6:44 PM, Chandan Choudhury wrote: > > Dear gmx_users, > > I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the > PBC. e.g. I

[gmx-users] g_msd and pbc

Dear gmx_users, I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the PBC. e.g. If I want to calculate the lateral diffusion of a lipid bilayer and at some point of the trajectory, some lipid molecules, due to PBC in the lateral direction, might pop out from one side of the box