[gmx-users] Water_polarization error

[Mark Abraham]

Hi,

Please keep the discussion on the mailing list. Others may have the same
problem, or know the solution ;-)

That sounds like a bug in the way grompp tries to work out what parameters
you are giving it. Can you please open an issue at
http://redmine.gromacs.org and upload a set of input files in a tarball so
we can take a look?

Thanks,

Mark

On Tue, Aug 4, 2015 at 4:56 PM amit sharma <amit_sps2004 at yahoo.co.uk> wrote:

> Hi,
>
> This Water_polarization error do come even if try to use any kind of flat
> bottom restrain on a simple system like mono atoms in a box.
>
> I paste here the last few lines of grompp output may be you have any idea
> which could help
>
> "Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
> Ignoring obsolete mdp entry 'domain-decomposition'
> Ignoring obsolete mdp entry 'andersen_seed'
> Ignoring obsolete mdp entry 'dihre'
> Ignoring obsolete mdp entry 'dihre-fc'
> Ignoring obsolete mdp entry 'dihre-tau'
> Ignoring obsolete mdp entry 'nstdihreout'
> Ignoring obsolete mdp entry 'nstcheckpoint'
> Replacing old mdp entry 'unconstrained-start' by 'continuation'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
>
> NOTE 1 [file 300k.mdp]:
>   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>   nstcomm to nstcalcenergy
>
>
> NOTE 2 [file 300k.mdp]:
>   The Berendsen thermostat does not generate the correct kinetic energy
>   distribution. You might want to consider using the V-rescale thermostat.
>
> Generated 1 of the 1 non-bonded parameter combinations
>
> -------------------------------------------------------
> Program grompp, VERSION 4.6.5
> Source code file: /build/buildd/gromacs-4.6.5/src/kernel/topdirs.c, line:
> 212
>
> Fatal error:
>
> Water polarization should now be listed under [ water_polarization ]
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ------------------------------------------------------- "
>
> Thanks,
>
> Amit
>
> ------------------------------
> *From:* Mark Abraham <mark.j.abraham at gmail.com>
> *To:* gmx-users at gromacs.org; amit sharma <amit_sps2004 at yahoo.co.uk>; "
> gromacs.org_gmx-users at maillist.sys.kth.se" <
> gromacs.org_gmx-users at maillist.sys.kth.se>
> *Sent:* Monday, 3 August 2015, 18:48
>
> *Subject:* Re: [gmx-users] Water_polarization error
>
> 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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