How does "-[no]correct (no)" flag works in gmx potential tool?

User discussions
1

GROMACS version:22.4
GROMACS modification: No

Hi,

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.

Screenshot From 2025-01-29 22-22-02
Screenshot From 2025-01-29 22-22-021418×733 31.9 KB

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.

Thank you
Prithvi

2

It looks like the right one is run with -symm, but not the left one.

Edit: Actually it doesn’t look like it’s symmetrized. My mistake. But it looks like the right one is run with -center, but not the left one.

3

Thanks for the reply,

Yes, the left one is without -center flag, but even if I include the -center flag the graph does not change, as shown below:

Screenshot From 2025-01-30 12-15-27
Screenshot From 2025-01-30 12-15-27699×752 5.59 KB

4

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?

5

Here are the exact commands for the above plots:
Left plot of figure-1:

gmx potential -f prd.0.xtc -n index_2.ndx -s prd.0.tpr -o potenial_sys_l_50ns_3.xvg -oc charge_sys_l_50ns_3.xvg -of field_sys_l_50ns_3.xvg -sl 100 -b 50000 -e 100000
Right plot of figure-1:
gmx potential -f prd.0.xtc -n index_2.ndx -s prd.0.tpr -o potenial_sys_l_50ns_3.xvg -oc charge_sys_l_50ns_3.xvg -of field_sys_l_50ns_3.xvg -sl 100 -b 50000 -e 100000 -center -correct

figure-2:

gmx potential -f prd.0.xtc -n index_2.ndx -s prd.0.tpr -o potenial_sys_l_50ns_3.xvg -oc charge_sys_l_50ns_3.xvg -of field_sys_l_50ns_3.xvg -sl 100 -b 50000 -e 100000 -center

figure-3(shown below, with symmetry):

gmx potential -f prd.0.xtc -n index_2.ndx -s prd.0.tpr -o potenial_sys_l_50ns_3.xvg -oc charge_sys_l_50ns_3.xvg -of field_sys_l_50ns_3.xvg -sl 100 -b 50000 -e 100000 -center -symm

Screenshot From 2025-01-30 15-14-10
Screenshot From 2025-01-30 15-14-10699×752 6.25 KB

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.

6

Thanks for the command lines and output with symmetry.

Neither am I. Hopefully, someone with more knowledge about the tool can bring some clarity.