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Erik Marklund

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03/28/2017

11:44 AM GROMACS Bug #2148 (Feedback wanted): gmx solvate crashing or leaving gaps for hexagonal solvent box
e are trying to merge a box containing a peripheral membrane protein with another box generated with memgen. Both box...

04/20/2016

08:46 PM GROMACS Bug #1949: gmx solvate leaves empty temporary files (as do other gmx programs)
Linux (CentOS).
03:07 PM GROMACS Bug #1949: gmx solvate leaves empty temporary files (as do other gmx programs)
Turns out that genion also does this for me. Perhaps this is an issue with my gmx executable? Will diagnose further.
03:01 PM GROMACS Bug #1949 (Closed): gmx solvate leaves empty temporary files (as do other gmx programs)
When running gmx solvate I end up with a file #temp.topoAUcbx.1# (or similar), which is empty, in addition to the exp...

02/14/2015

10:52 AM GROMACS Revision aa1cfd57: gmx hbond no longer removes PBC when none is present
Fixes #1662
Change-Id: Ice934285784ac8b8fd95942a089fb1b65b9ecb51

01/13/2015

04:08 PM GROMACS Bug #1668 (Rejected): Incorrect PBC removal in gmx hbond
The description is incorrect. PBC removal should be along box vectors. This issue furthermore only arose in a now aba...

01/07/2015

11:28 PM GROMACS Bug #1668 (Rejected): Incorrect PBC removal in gmx hbond
The PBC removal in gmx hbond appears to be done along the box vectors instead of orthogonal vectors. pbc_correct_gem(...

01/06/2015

04:02 PM GROMACS Bug #1662: g_hbond not running
The bug is there in release-5-0. I'll fix it and try to backport to release-4-6.
11:05 AM GROMACS Bug #1662: g_hbond not running
I think this is related to the absence of pbc and I can reproduce this with other gas-phase trajectories. (Why doesn'...

05/26/2014

12:09 AM GROMACS Feature #1511 (Closed): add PDBx (ie mmcif) support

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