[gmx-users] Facing poblem in enegy minimization step

[Tsjerk Wassenaar]

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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