GROMACS development

03/20/2019

02:17 PM GROMACS Bug #2879: Virial and pressure completely incorrect with SHAKE

Mark Abraham wrote:
> Berk Hess wrote:
> > Thanks Artem, but I/we already knew this is the issue. This is what Mark...

01:43 PM GROMACS Task #2898: Naming common variables

Eric Irrgang wrote:
> Is the idea that these are variable names that frequently get reused and should therefore have...

03/19/2019

04:07 PM GROMACS Task #2898: Naming common variables

Kevin Boyd wrote:
> One suggestion - I'd naively interpret computeVirial and compte_dHdLambda as a verb, so that see...

01:18 PM GROMACS Task #2898 (New): Naming common variables

One of the most complicated problem to a programmer is to figure out how to name a variable, a function, a class or a...

10:57 AM GROMACS Bug #2879: Virial and pressure completely incorrect with SHAKE

I think I found the bug:
In bshakef(...) function in shakef.cpp, when the computations are split to blocks, all bl...

03/13/2019

07:10 PM GROMACS Feature #2888: CUDA Update and Constraints module

I have LINCS with some tests for it, SETTLE with some tests for it and Leap-Frog integrator with some tests for it. N...

02:46 PM GROMACS Revision 39f66f14: Basic routines to handle periodic boundary.

This is a generalization of the SIMD/GPU-like PBC
routines so that they can be used in a CPU code as well.
(Related ...

03/08/2019

04:23 PM GROMACS Feature #2816: Device-side update&constraits, buffer ops and multi-gpu comms

I've created blank features for the GPU-only loop. Will start filling them up .

04:22 PM GROMACS Feature #2888 (New): CUDA Update and Constraints module

* -LINCS for non-water constraints.-
* -SETTLE for water constraints.-
* -Leap frog integrator.-
* -Merge of the t...

04:21 PM GROMACS Feature #2887 (New): CUDA version of Leap Frog algorithm

The initial implementation works independently from other parts of the code, which require a temporary infrastructure...