I was trying to perform an MD of a protein (Mrgprx2) in a lipid bilayer. The domain of the protein looks like this: Thus I’d like to have the transmembrane part of the protein to be buried in lipid membrane, and the extracellular part of it to be placed outside membrane. I was following the Gromacs Membrane Protein Tutorial. However the protein orientation I get is not as…

GROMACS version: 2021.4-Ubuntu-2021.4-2 GROMACS modification: No Hi everyone! Does anyone have information on how the position restraints of atoms affect the calculation of the surface tension of a SAM on a metallic layer? The case is quite specific, even general information already helps. Any informative source, formula, explanation…anything helps currently. You can find a lo…

GROMACS version:2021.4 GROMACS modification: no gmx grompp -f npt_umbrella.mdp -c conf449.gro -p topol.top -r conf449.gro -n index.ndx -o npt22.tpr -maxwarn 1 when i tried to run this command in umbrella sampling tutorial ,its giving the following error: NOTE 3 [file npt_umbrella.mdp]: Removing center of mass motion in the presence of position restraints might cause artifacts…

GROMACS version:2022-03 GROMACS modification: No I am trying to determine the Potential of mean force profile for a ligand passing through a membrane. I was planning to use gromac’s AWH tool. I would like to pull the ligand through the entire membrane (more than half the box). However, I keep getting error messages indicating that this is not permitted. What mdp parameters do I …

GROMACS version: GROMACS modification: Yes/No Here post your question gmx grompp -f em.mdp -p topol.top -c solvate -o em.tpr Ignoring obsolete mdp entry ‘ns_type’ NOTE 1 [file em.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed …