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Vytautas Gapsys

  • Email: vgapsys@gwdg.de
  • Registered on: 08/08/2018
  • Last connection: 03/21/2020

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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 (Accepted): 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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