General

Profile

Vytautas Gapsys

  • Email: vgapsys@gwdg.de
  • Registered on: 08/08/2018
  • Last connection: 10/14/2019

Issues

Activity

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...

Also available in: Atom