GROMACS version: 5.1.4 (single precision)
GROMACS modification: Yes
Hello all,
I am having a bit of trouble with a simple MD simulation I am trying to set up. In my system I only have two separate residues, called ACEM and MAMM by the CHARMM force field. MAMM is methyl ammonium and so has a positive charge that needs to be neutralized. However when I run
gmx genion -s ions.tpr -o (output file) -p topol.top -pname SOD -nname CLA
It doesn’t do anything, saying that there are no ions to add.
Even stranger to me, when I move on to making the .tpr file for energy minimization, I get a note stating the system is charged with the correct charge of 1. From this it seems that GROMACS seems to have some recognition of the charge, but doesn’t use it or loses this info when adding ions. Any help would be appreciated.
You haven’t told genion to do anything. You need to tell it to neutralize the charge with -neutral or specify a concentration of ions with -conc.
Thank you very much, glad to know it was something simple.