[gmx-users] Problem with gmx genion

[Live King]

Dear all,

I am using martini polarisble FF and I have generated mixed lipid bilayer
containing (DOPC-DOPS).
I am trying to neutralise  the system by adding NA using this commnad

*gmx genion -s ions.tpr -o ionized.gro -p topol.top -pname NA -nname CL
-neutral*

I replace PW (water molecules) with NA and system gets successfully
neutralised. My bilayer bilayer is fully symmetric but the distribution of
ions generated by genion is not.

See the VMD output.

*set sel [atomselect top "resname NA and z > 79"]*

*atomselect0*

* $sel num*

*17*

set sel [atomselect top "resname NA and z < 79"]

atomselect2

 $sel num

15

--------------------------------------------

Just to confirm that my bilayer is symmetric.


set sel [atomselect top "resname DOPS and z < 79"]

atomselect4

 $sel num

192


set sel [atomselect top "resname DOPS and z > 79"]

atomselect5

$sel num

192

---------------------------------------------


Is it a potential bug in genion or am I doing something wrong  ?



Thanks,

Vikas