[gmx-users] Water molecule can not be settled

[Billy Williams-Noonan]

Hi Mark,

Late response.  I meant reducing the emstep parameter.  I've found this
helps with minimising water molecules that are too close together.  That or
you could manually shift the relevant waters and re-minimise. Apologies for
the typo.  Looks like the problem is sorted now.

Billy

On 1 July 2016 at 02:22, Mark Abraham <mark.j.abraham at gmail.com
<javascript:_e(%7B%7D,'cvml','mark.j.abraham at gmail.com');>> wrote:

> Hi,
>
> Run with one rank, e.g. gmx mdrun -ntmpi 1
>
> Mark
>
> On Thu, Jun 30, 2016 at 6:11 PM zeineb SI CHAIB <zeineb-14 at hotmail.com
> <javascript:_e(%7B%7D,'cvml','zeineb-14 at hotmail.com');>>
> wrote:
>
> > Dear Mark,
> >
> > Thank you for your orientation. I looked in Google and based on what you
> > advised me, I prepared the following mdp file
> >
> > integrator = steep
> > nsteps = 1000
> > emtol = 1000.0
> > emstep = 0.01
> > energygrps    = system
> >
> > pbc         = no
> > nstlist = 0
> > ns-type = simple
> > rlist       = 0
> >
> > cutoff-scheme = group
> > coulombtype              = cut-off
> > rcoulomb                 = 0
> > vdw-type                 = Cut-off
> > rvdw                     = 0
> >
> >
> > However, I'm working with GROMACS 5.1.2 and apparently some combinaisons
> > doesn't work. When I run EM with these mdp parameters I got the following
> > error:
> >
> > Fatal error:
> > Domain decomposition does not support simple neighbour searching, use
> grid
> > searching or run with one MPI rank
> >
> > Is there a problem with these parameters?
> >
> > Zeineb
> >
> > --
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-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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**|*   +61420 382 557

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-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052