[gmx-users] Problem with gmx genion

[Justin Lemkul]

On 10/7/16 4:10 AM, Live King wrote:
> 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  ?
>

genion adds ions randomly.  It doesn't care about symmetry.  But in reality, the 
system is symmetric, because it is periodic.  There are no distinct "sides" of a 
membrane in a system with PBC.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================