Re: [gmx-users] WARNING: Listed nonbonded interaction between particles X and Y at distance

Hi, Make sure your particles have vdw on before you add charge to them. That's usually the cause of this problem. Mark On Mon, Apr 16, 2018, 20:51 faride badalkhani wrote: > Dear all, > I am trying to perform free energy calculations of a small drug in octanol >

[gmx-users] WARNING: Listed nonbonded interaction between particles X and Y at distance

Dear all, I am trying to perform free energy calculations of a small drug in octanol using the GROMACS 5.1.3 software. I built a box of octanol using the following command gmx insert-molecules -ci oct.gro -nmol 125 -box 4 4 4 -o oct_box.gro Followed by steepest descent minimization, 100 ps each