[gmx-users] Damping for pulled group

Alex nedomacho at gmail.com
Tue Jul 18 22:47:18 CEST 2017

I mean would it be hard to add a damping term. Sorry, half asleep. :)


On Tue, Jul 18, 2017 at 2:44 PM, Alex <nedomacho at gmail.com> wrote:

> 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,
> Alex

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