[gmx-users] Water_polarization error

amit sharma amit_sps2004 at yahoo.co.uk
Mon Aug 3 18:11:00 CEST 2015

In a cubic simulation box, I have a membrane protein system where lipid bilayer is mimicked with a belt (of desired width and radius) of mono-atoms. And, the left over box is filled with water molecules. 

Mono-atoms surrounding the protein molecule are held through non-bonded Lenard Jones interaction with the protein Carbon atoms. In order to have a belt of desired width, I am applying flat bottom position restraint in a plane with its normal parallel to protein axis.
Position restraint applied on a LJ potential is defined as follows: 
"[ position_restraints ]
; ai  funct     g      r(nm)   k(KJ/mol/nm^2)
   1    2       5       1      100   ; flat bottom position restrain to a z plane"
On executing a grompp command using a topology containing this restraint, I get the following error

"Water polarization should now be listed under [ water_polarization ]"

Any idea on how to deal with this error could be of great help?
Thank You,



More information about the gromacs.org_gmx-users mailing list