General

Profile

Berk Hess

Issues

Projects

Activity

08/16/2017

10:14 PM GROMACS Revision 0e49e198: Add dynamic pair-list pruning framework
The change add the logistic for setting up dynamic pruning of the
nbnxn pair-lists. Dynamic pruning allows for an inc...
06:25 PM GROMACS Revision 6ca52dcf: Clean up nbnxn cluster pair addition code
Partial clean up of the nbnxn CPU makeClusterList functions.
Clarified variable names and added more documentation.
N...
04:19 PM GROMACS Bug #2228 (Resolved): PBC issue with orientation restraints and the Verlet scheme
Applied in changeset commit:899b4c2e92100e449c81dde33476e9fbafed08fd.
02:14 PM GROMACS Bug #2201 (Resolved): Constraint COM pull forces incorrect with SD integrator
A fix has been merged into release-2016. With this fix the friction and random forces are still included in the pull ...
01:57 PM GROMACS Feature #2218: A tiny feature: damping for umbrella pull
Ah, now I understand. I didn't realize you have an actual AFM tip consisting of atoms. I am used to pulling with some...

08/15/2017

10:36 PM GROMACS Revision 1c9c1d1b: Add OpenMP for orientation restraints
Recent commit 0be497b7 disabled OpenMP for orientation restraints.
Now the restraint indexing issue with OpenMP is re...
10:35 PM GROMACS Revision 899b4c2e: Use graph with orientation restraints
With the Verlet cut-off scheme by default molecules are not made whole.
Now they are made whole when orientation rest...

08/12/2017

10:55 PM GROMACS Revision 5e2d0e63: Remove loop over all atoms in init_mdatoms
We should avoid non-parallel loops over all atoms in the system.
Change-Id: I7052f7f203e7d191377ab939e26f9dcd713a9998

08/10/2017

02:40 PM GROMACS Feature #2218: A tiny feature: damping for umbrella pull
I don't know if I understand anymore. If the tip is supposed to be damped, this has nothing to do with the COM of the...

08/09/2017

08:57 AM GROMACS Feature #2218 (Feedback wanted): A tiny feature: damping for umbrella pull

Also available in: Atom