GROMACS version: 2020.4 GROMACS modification: No Hi, I’m trying to set up my simulations so that all water molecules are not allowed to get close to a defined water molecule in the binding site (with a distance cutoff). I think an inverted flat bottomed position restrict is a good choice. But as far as I understand, the flat-bottomed position restraints implemented in GROMACS on…

GROMACS version: 2021.4 GROMACS modification: No Dear gmx users, I wonder if the settings of the thermostat and barostat are dependent on the force field or not. Is there a proper combination of tcoupl and tau-t, pcoupl and tau-p for each force field? By testing various combinations of algorithms and coupling times, Can I simply select a combination with a low Err. Est. or RMS…

GROMACS version: GROMACS modification: Yes/No Here post your question Hello everyone, I am trying to vary the viscosity of the water solvent by varying its mass. I tried looking up materials online but was not successful and went through gmx solvate man page. Could someone please suggest how the general protocol goes for varying the viscosity of a solvent in GROMACS? …

GROMACS version: 2018.6 GROMACS modification: No Hello, I am trying to do free energy perturbation (FEP) calculations in implicit solvent (GB), but this throws the fatal error “Free energy and GB not implemented.” in gmx mdrun. Is it not possible to use the implicit solvent model on free energy calculations for any version of gromacs? My motivation for these calculations is to o…

GROMACS version: 2020 GROMACS modification: Yes How to extend a PLUMED metadynamics run? My run abruptly stopped at 38ns and I need to extend it instead of starting afresh. It’s only using one GPU as of now (instead of available 4) but that’s an issue for another day… 1 post - 1 participant Read full topic

GROMACS version: 2018 GROMACS modification: No Greetings I want to perform ion channel MD simulations using gromacs. My objective is to study the inhibition of permeation of K+ ion through the channel by the ligand. The tetramer of Kcsa protein is created using vmd (pdb id - 1k4c) with K+ ions in the channel. the water molecules are removed from the cavity The ligand under st…

GROMACS version: GROMACS modification: Yes/No Here post your question ’ I have 10 drug molecules from FDA (not in any databases) for which I want to perform MD Simulations. Somehow not able to generate the topology file for the drugs (ligands) due to their unsatisfied valances. Can you suggest or guide me to generate a simulation without an STR file for these unknown molecules?…