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Thomas Ullmann

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02/08/2019

12:44 PM GROMACS Revision 188429af: separated .rst documentation of dihedral PCA and hydrogen-bonds
The section of the reference manual on hydrogen-bonds was included
in dihedral-pca.rst. This hindered insertion of a ...

02/06/2019

10:59 PM GROMACS Revision c95b5530: added a unit test for make_ndx to check generation of default protein index groups
Change-Id: I56b26a7eefeb818ec038696b8bb9e3a47e9ac536

02/05/2019

07:51 PM GROMACS Revision 0db3eb52: Fix bug in generating default protein index groups
The bug was introduced in 3c3dd54f00. When recording
atom indices for an index group in a temporary
vector, the indic...

12/04/2018

11:54 PM GROMACS Feature #2791 (In Progress): Implement a module for lambda-dynamics simulations (lambda_site module)
h2. Purpose
This issue gathers information about the ongoing development of a lambda-dynamics module for GROMACS t...

11/12/2015

02:46 AM GROMACS Bug #1853 (Closed): LINCS: (erroneous?) assertion with multiple tMPI ranks and multiple OpenMP threads
When running with more than one tMPI thread and more than one one OpenMP thread per rank,
I get the following error ...

03/24/2015

09:40 PM GROMACS Feature #1653: Decide how to represent multiple lambda states in the .top file and how to parse them
I'm planning to prepare some draft commits in the near future.
However, you can also have a look at the entire code ...
03:42 PM GROMACS Feature #1653: Decide how to represent multiple lambda states in the .top file and how to parse them
Sounds great, thanks for offering help! I will ask for your opinion on my solution as soon as I arrive at this point,...

12/12/2014

04:34 PM GROMACS Feature #1653: Decide how to represent multiple lambda states in the .top file and how to parse them
>Note that in any program that includes lambda dynamics, there is some history dependent information.
>Most methods ...

12/11/2014

09:49 PM GROMACS Feature #1653: Decide how to represent multiple lambda states in the .top file and how to parse them
For the output, I think that it would be most general to state the value of the lambda variable for each form of each...

12/10/2014

01:20 AM GROMACS Feature #1653: Decide how to represent multiple lambda states in the .top file and how to parse them
??Could you define what you mean by a form ID? We need to be more precise in definitions. I'm guessing it has to do w...

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