[gmx-users] diffusivity computations

Hi all, I have been trying to estimate the diffusivity of an alanine molecule in water with the .mdp file (for md simualtions) given below. When I plot the mean square displacement, however I do not see a linear variation with time (which is what I expected). Moreover, the estimated

[gmx-users] dialanine

Hi, I am seeking help in creating the .pdb file for a dialanine molecule using the databank. I have the parameters for a single alanine molecule. how do i go from here. Thanks Debashis ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] diffusivity computations

Hi, I have trying to estimate the diffusivity of an alanine molecule in water with the following .mdp file (for md simualtions). ; Preprocessing title = Alanine with Water cpp = /lib/cpp include = define = ; Run Control integrator