[gmx-users] Water_polarization error
mark.j.abraham at gmail.com
Mon Aug 3 18:48:36 CEST 2015
Could be a code bug. Are you using normal water and doing normal MD?
On Mon, Aug 3, 2015 at 6:11 PM amit sharma <amit_sps2004 at yahoo.co.uk> wrote:
> 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,
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