Vytautas Gapsys
- Email: vgapsys@gwdg.de
- Registered on: 08/08/2018
- Last connection: 06/23/2020
Issues
Activity
03/21/2020
- 09:28 PM GROMACS Bug #3403: solvation free energy with couple-intramol set to no
- Berk Hess wrote:
> Note that table-extension does nothing in release-2020 which only supports the Verlet cutoff-sc...
02/27/2020
- 05:41 PM GROMACS Bug #3403: solvation free energy with couple-intramol set to no
- A possible issue when calculating solvation free energies and using the option: couple-intramol = no
The observati... - 05:34 PM GROMACS Bug #3403 (Resolved): solvation free energy with couple-intramol set to no
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...
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