I have a simple membrane bilayer system, where POPC is the membrane lipid and is equilibrated with 150mM KCL, and the net charge of the whole system is zero.
I am trying to get the electrostatic potential of the system across the z-axis using the tool gmx potential.
When I use the gmx potential command without -correct flag (gmx potential -f prd.0.conv.xtc -n index_2.ndx -s prd.0.tpr -o potenial_sys_2.xvg -oc charge_sys_2.xvg -of field_sys_2.xvg -sl 100 -center), I get following plot as shown in left side of the figure.
When I use the gmx potential command with -correct flag (gmx potential -f prd.0.conv.xtc -n index_2.ndx -s prd.0.tpr -o potenial_sys_2.xvg -oc charge_sys_2.xvg -of field_sys_2.xvg -sl 100 -center -correct), I get the plot shown in right of the figure.
Since my system’s net charge is already zero, I don’t understand why I get two different results in these two cases (I think both cases should give the same results.). Can anyone please explain the reason behind this?
Also, if there is any reference towards the workings of the command and related flag, please redirect me.
OK. So the commands you showed above were not exactly correct. Are there any other differences in the commands? At least they’re more similar with -center. What would it look like with -symm? I’m not sure why -correct would make a difference, but I haven’t used gmx potential much.
From the output, my impression is that you might need to simulate (and/or equilibrate) longer to get rid of the overall tilt of the potential curve. How long is your current simulation and for how long was it equilibrated?
I have done 15 ns of equilibration followed by 100 ns of production run. The system size is around ~45K atoms, and the box length is 6.7nmX6.7nmX9.6nm.
Even if it has not equilibrated properly and charges are distributed such that I get a potential plot like in figure-2, I am not sure why I am getting a different plot for -correct flag, for a system with a zero net charge.