[gmx-users] Error message in Energy minimization

[Deep Bhattacharya]

It did run but it gave a note

NOTE 2 [file topol.top]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Please help.

Deep

*Deep S Bhattacharya*
Graduate Research Assistant,
Department of Pharmaceutical sciences,

University of Nebraska Medical Center

Cell: (402) 906-8422
Work: (402) 559-4349

Email:  deep.bhattacharya at unmc.edu, deep.bhattacharya1991 at gmail.com


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On Wed, Jul 13, 2016 at 10:57 AM, Evan Lowry <evanwlowry at gmail.com> wrote:

> Yes, that is possible. It should run.
>
> Evan L.
>
> On Jul 13, 2016 9:47 AM, "Deep Bhattacharya" <
> deep.bhattacharya1991 at gmail.com> wrote:
>
> >
>
> > That would be rcoulumb rvdw and rlist at 1.4.
> > Is that possible?
> >
> > Deep
> >
> > Sent from my iPhone
> >
> > > On Jul 13, 2016, at 10:45 AM, Evan Lowry <evanwlowry at gmail.com> wrote:
> > >
> > > Set rcoulomb=rlist and retry the minimization.
> > >
> > > Evan L.
> > > On Jul 13, 2016 9:38 AM, "Deep Bhattacharya" <hypergenetics at gmail.com>
> > > wrote:
> > >
> > >> Hello,
> > >>
> > >> This is the error message that I am getting trying to run energy
> > >> minimization
> > >>
> > >> ERROR 1 [file em.mdp]:
> > >>  With coulombtype = PME (without modifier), rcoulomb must be equal to
> > >>  rlist,
> > >>  or rlistlong if nstcalclr=1. For optimal energy conservation,consider
> > >>  using
> > >>  a potential modifier.
> > >>
> > >> em.mdp
> > >>
> > >> ; minim.mdp - used as input into grompp to generate em.tpr
> > >> define       =  -DPOSRES -DPOSRES_LIGAND
> > >> integrator = steep
> > >> emtol = 1000.0
> > >> emstep      = 0.01
> > >> nsteps = 500000
> > >> energygrps              = System
> > >> nstlist    = 1
> > >> rlist               = 1.4
> > >> ns_type    = grid
> > >> coulombtype    = PME
> > >> rcoulomb    = 0.9
> > >> vdwtype        = cut-off
> > >> rvdw    = 1.4
> > >> pbc    = xyz
> > >> epsilon-rf     = 61
> > >>
> > >>
> > >> Please help.
> > >>
> > >> *Deep S Bhattacharya*
> > >>
> > >> *Graduate Research Assistant*
> > >>
> > >> Mohs Biomedical Imaging & Nanotechnology Group
> > >>
> > >> Pharmaceutical Sciences
> > >>
> > >> *University of Nebraska Medical Center*
> > >>
> > >> 4018 Eppley Science Hall  |  Omaha, NE 68198-6805
> > >>
> > >> office 402.559.4349  | cell 402.906.1640
> > >>
> > >> deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com
> > >> --
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