Dear Gromacs users,
I'm adding two different salts to my system in different concentrations;
first salt addition is done successfully using the following commands:
>gmx grompp -f em.mdp -c sys_solv.gro -p topol.top -o ions.tpr
>gmx genion -s ions.tpr -o sys_solv_ions.gro -p topol.top -pname MG
"Maximum force =inf on atom 3999"
is the hint Gromacs gave you. This means that atom 3999 (and possibly more)
have very bad overlaps. This is backed up by your LJ energy being very high.
Use VMD (or something similar) to inspect that atom and it's surrounding.
Peter
On 16-09-19
Dear all,
I am interested in carrying out a simulation of mPGES-1 protein (PDB id:
4yl3), which is a homotrimer. I am using POPC membrane; equilibrated for
100 ns for this purpose. I was able to align and insert the protein into
the membrane using lambada align and inflategro programs,
