[gmx-users] Damping for pulled group

Justin Lemkul jalemkul at vt.edu
Wed Jul 19 03:17:48 CEST 2017

On 7/18/17 4:44 PM, Alex 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?

Code issues can be discussed on the gmx-developers mailing list.  Feature 
requests can be made on redmine.gromacs.org.  The best case is to file the 
feature request, take it on yourself, and discuss any issues on gmx-developers :)



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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