[gmx-users] Damping for pulled group

Alex nedomacho at gmail.com
Tue Jul 18 22:44:23 CEST 2017

Hi all,

This is more of a question about where I should make a suggestion for the
developers. It turns out that Gromacs pull code was designed nearly
perfectly to do simulated friction force microscopy (FFM), i.e. scanning a
surface with a tip. The only thing that's missing is that the equation of
motion for the pulled group's COM does not contain an artificial damping
term and the group is free to oscillate, which is a common occurrence in
underdamped situations even experimentally. For pulling in systems GMX was
designed for, the lack of additional damping makes perfect sense for things
that are immersed in solvents (which would readily provide any damping),
but most simulated FFM is in vacuum. Options other than umbrella are
physically flawed, unfortunately.

Would it had to add a damping term for the umbrella and where should I post
this request for the developers?

Thank you,


More information about the gromacs.org_gmx-users mailing list