[gmx-users] Water_polarization error
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?
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