[gmx-users] Water_polarization error

[Mark Abraham]

Hi,

Could be a code bug. Are you using normal water and doing normal MD?

Mark

On Mon, Aug 3, 2015 at 6:11 PM amit sharma <amit_sps2004 at yahoo.co.uk> wrote:

> Hi,
> 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,
>
> Amit
>
>
>
>
>
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