GROMACS development

10/18/2019

06:03 PM GROMACS Bug #3074: box volume is affected by decoupled molecule when using couple-moltype mdp option

> I don't know. I would say that in most cases the issue is using constraints=all-bonds. Most force fields are not ...

10:44 AM GROMACS Bug #3074: box volume is affected by decoupled molecule when using couple-moltype mdp option

Indeed, higher order LINCS setting removed the box size dependence for free energies (dg_updated_lincs.png) and volum...

10/17/2019

09:47 AM GROMACS Bug #3074: box volume is affected by decoupled molecule when using couple-moltype mdp option

The free energy summary is now attached (dg.png).
mdp decoupling with couple-intramol=yes has the same behavior as t...

10/15/2019

07:01 PM GROMACS Bug #3074: box volume is affected by decoupled molecule when using couple-moltype mdp option

To my understanding, the energy analysis shows the expected results (attached average_energies.png).
The overall d...

10/14/2019

10:06 PM GROMACS Bug #3074: box volume is affected by decoupled molecule when using couple-moltype mdp option

I considered this option as well, however, with the couple-intramol=yes the effect remains: attached is again volume ...

09:20 PM GROMACS Bug #3074: box volume is affected by decoupled molecule when using couple-moltype mdp option

True, this might happen depending on a molecule. However, in the current situation this is not the case: attached is ...

06:49 PM GROMACS Bug #3074: box volume is affected by decoupled molecule when using couple-moltype mdp option

mdp_decoupling uses only one leg of the cycle. Since couple-intramol flag is set to "no", the decoupled state corresp...

06:25 PM GROMACS Bug #3074: box volume is affected by decoupled molecule when using couple-moltype mdp option

For the itp_decoupling, vacuum-leg of the cycle uses the same topology as water-leg (attached).

09/04/2019

07:28 PM GROMACS Bug #3074 (Rejected): box volume is affected by decoupled molecule when using couple-moltype mdp option

Alchemically decoupled molecule (via .mdp option couple-moltype) affects the box volume, i.e. at constant pressure th...

08/14/2019

02:08 PM GROMACS Bug #3056: Miscalculated LJ(SR) when running with GPU?

The difference between CPU and GPU LJ-SR disappears when rcoulomb and rvdw are set to the same value (tested with 201...