[gmx-users] Facing poblem in enegy minimization step

[Tsjerk Wassenaar]

Hi Swagata,

That's when the potential energy remains high and/or the maximum force is
still large.

Cheers,

Tsjerk

On Sat, Jul 16, 2016, 12:27 Swagata Patra <swagataliza at gmail.com> wrote:

> Thank you very much Tsjerk.
>
> Actually I searched in google and somewhere i read that it might be because
> either the topology is bad or the starting structure has clashes that
> cannot be adequately addressed using EM or because of improper
> parametrization.
>
>
> On Sat, Jul 16, 2016 at 3:43 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > Hi Swagata,
> >
> > That's not a problem. You should be fine running a simulation, given the
> > potential energy of the system. Check the archives for more elaborate
> > comments on this matter. And please check the archives/google before
> > posting questions. We like breaking our heads over new, tough issues, and
> > don't really fancy chewing on old matters, which come up on a monthly
> > basis.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Jul 16, 2016 12:08 PM, "Swagata Patra" <swagataliza at gmail.com> wrote:
> >
> > > Hello evryone,
> > >
> > > I am tying to do simulation of a protein-ligand complex. But in energy
> > > minimization step I am facing the following problem:
> > >
> > >
> > > Stepsize too small, or no change in energy.
> > > Converged to machine precision,
> > > but not to the requested precision Fmax < 1
> > > You might need to increase your constraint accuracy, or turn
> > > off constraints alltogether (set constraints = none in mdp file)
> > >
> > > writing lowest energy coordinates.
> > >
> > > Steepest Descents converged to machine precision in 37686 steps,
> > > but did not reach the requested Fmax < 1.
> > > Potential Energy  = -1.22228866049133e+06
> > > Maximum force     =  1.60313450715092e+02 on atom 1628
> > > Norm of force     =  1.38085169243203e+00
> > >
> > > i prepared the ligand topology file using ATB. There I was getting an
> > > warning like : "This molecule contains non-standard atom types not
> > included
> > > in the standard GROMOS 53A6 and 54A7 forcefield. To use these atom
> types
> > > the internal GROMACS parameter files must be updated. These can be
> > > downloaded using the link below. So I donloaded the filee and also
> modify
> > > it in topology file.
> > >
> > > Please help me to overcome the problem.
> > > I am attaching the topology file.
> > >
> > > --
> > > Swagata Patra
> > > M.Tech (Biotech)
> > > JRF
> > > IIT Guwahati
> > >
> > > --
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>
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
> --
> Gromacs Users mailing list
>
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