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Semen Yesylevskyy

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09/13/2019

11:26 AM GROMACS Bug #3088 (New): Reference to theory needed for cylindrical pull geometry
Cylindrical pulling is a non-trivial thing in terms of the theory but the manual is very scarce on it.
If one googl...

09/04/2019

08:00 PM GROMACS Bug #3075 (New): Frozen atoms are moving
This bug is mysterious for me because I can't isolate it in a minimal system, so I apologize for complex and messy ex...

08/26/2019

03:44 PM GROMACS Bug #3068 (New): Misleading warning on rerun
When doing `mdrun -rerun` with multiple energy groups the following warning is issued:...

05/15/2019

09:02 AM GROMACS Feature #2946: Enable AWH periodicity for pull-geometry=direction
Yes, it seems to work correctly now on my system.

05/14/2019

09:36 AM GROMACS Feature #2946: Enable AWH periodicity for pull-geometry=direction
It doesn't work for me. See attached example. The box size on Z is 10.9827 and awh range is (-6:6). In log file there...

05/13/2019

01:16 PM GROMACS Feature #2946: Enable AWH periodicity for pull-geometry=direction
Is there a possibility to allow periodicity for arbitrary pull vectors (not aligned with one of the axes?). I'm not a...
12:37 PM GROMACS Feature #2946: Enable AWH periodicity for pull-geometry=direction
Under peridicity I mean making start and end points of interval the same point in PMF computation (an equivalent of -...

05/11/2019

11:48 AM GROMACS Bug #2949 (New): cmake fails when building mdrun only
When trying to compile mdrun only cmake fails:
$ cmake ../gromacs-git -DCMAKE_INSTALL_PREFIX=~/programs/gromacs-gi...
10:42 AM GROMACS Feature #2946: Enable AWH periodicity for pull-geometry=direction
Ok, but what about the question itself - how can the user define the periodic awh coordinate, say, across the simulat...

05/10/2019

09:52 AM GROMACS Feature #2946: Enable AWH periodicity for pull-geometry=direction
Digging the source code shows that function get_pull_coord_period() deduces periodicity for direction-periodic geomet...

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