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Erik Lindahl

  • Email: erik@kth.se
  • Registered on:
  • Last connection: 02/14/2018

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01/31/2018

02:49 PM GROMACS Bug #2388: inconsistent pinning behavior due to missing SMT info on AMD Zen
Well, it's not technically a bug since the hardware info module properly detects that we can't see it, and correctly ...

01/15/2018

04:24 PM GROMACS Feature #1842: Replace XML with JSON
Mark and I had another chat about JSON and our best strategies for it, partly based on recent development in JSON lib...

01/10/2018

12:39 PM GROMACS Bug #2370 (Resolved): pdb2gmx does not report why chains of residues are teminated
Applied in changeset commit:541e7d05da570755b263f5ada97215b96e61781c.
10:51 AM GROMACS Revision 541e7d05: Improve pdb2gmx for nonstandard residue types
If explicit non-blank chain identifiers are set, it
will now be a hard error if the residue types in each
chain do no...
09:30 AM GROMACS Revision 24db1d08: Clarified gmx rmsf documentation
Made it clearer what input files coordinates
are taken from when writing B-factors.
Fixes #2320.
Change-Id: Ic47cbb...

01/08/2018

12:15 AM GROMACS Task #2320 (Fix uploaded): documentation of gmx rmsf
12:02 AM GROMACS Bug #2205 (Closed): mdrun -cpi unable to find files despite correct location
Feel free to reopen if we missed something.
12:02 AM GROMACS Bug #2205 (Rejected): mdrun -cpi unable to find files despite correct location
I have played around a tested a few different things.
First, as long as you invoke mdrun exactly the same way in t...
10:50 AM GROMACS Task #2375: Clarify execution phases for MD simulation
For the first step, I think it will be much simpler to move/modify existing code so that all reading of input files a...

01/07/2018

12:00 AM GROMACS Bug #2125: Hexagonal PBC and MPI
Berk:
1) Is that only an issue at the start of a simulation, or could it ever be distorted to reach this shape du...

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