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Magnus Lundborg

  • Registered on: 03/12/2013
  • Last connection: 06/25/2020

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09/21/2020

11:07 AM GROMACS Revision 054bf288: AWH avoid constructors only differing in parameter types
Also clarified a function name in the tests.
Tests had to be updated since the force constant (now removed)
should no...

09/03/2020

01:35 PM GROMACS Revision 7d7cbb84: Print lambda state to log file if using AWH for FEP.
Change-Id: I08c7e6d51a299eb53556d5bde63c29f7c7640f6e

08/25/2020

03:01 PM GROMACS Revision 87516a80: Avoid log(0) if probability is too low
Change-Id: I96f5aa61f21303c4c382b8a0664cffd20e85bbd6

08/20/2020

02:15 PM GROMACS Revision 176671b9: Make it possible to use FEP lambda states as a reaction coordinate in AWH. Atom masses and constraints cannot be perturbed (yet). It is possible to use a multidimensional bias where the lambda state is one dimension. An AWH FEP lambda state dimension is always using a discrete Gibbs sampler (umbrella), even if another dimension is using a convolved bias potential.

07/20/2020

12:17 PM GROMACS Revision f7be07e3: Two sets of coefficients for Coulomb FEP PME on GPU
The first patch in a series to enable running Coulomb FEP PME on GPU.
Use two sets of coefficients to store atom char...

03/04/2020

10:40 PM GROMACS Revision 54d5fee7: Separate AWH parameter reading and checking
To avoid dependency on order of parameter reading (pulling
before AWH) AWH now reads parameters before checking them....

03/03/2020

10:37 AM GROMACS Revision 439bff03: Store dHdL for all neighbor lambdas
This is required for calculating forces along a lambda dimension
in AWH.
Change-Id: Ic5247a53998b1e733858419d20338b5...

03/01/2020

01:35 PM GROMACS Feature #2667: Suggested steps for calculating entropy in solution and binding
I don't know. I just requested this feature since I don't know the proper process and people wonder on different mail...

02/25/2020

06:43 PM GROMACS Revision ade8e131: Fix out of sync checkpoint files in simulations sharing state
When multidir simulations share the state, the checkpoint files
of the different simulations should all be from the s...

02/17/2020

03:58 PM GROMACS Feature #3117: Coulomb FEP PME on GPU
Yes, with an average over 3 runs (1000 steps) I think 47.3 ns/day vs 47.5 ns/day is just noise.

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