[gmx-users] diffusion coefficient

[Mark Abraham]

On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote:
> I want to calculate the diffusion coefficient of a small polypeptide 
> with g_msd (see here 
> http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant)
>
> because of periodic boundary condition, when the peptide goes out of 
> the right side it comes in from left side, which leads to an 
> artificial displacement. this will give rise to a non-realistic MSD.
>
> is g_msd intelligent enough to avoid this artificial displacement?
>

Not sure about g_msd, but you can take care of it yourself with a 
workflow derived from the information here 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark