[gmx-developers] Re: Re:Re:Re:Re:Re: Energy Minimization

[Igor Leontyev]

> I just noticed that settle for the coordinates (the forces were correct)
> does not support partially frozen water molecules.
> Try replacing in src/mdlib/mdatom.c:
>      if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] &&
> opts->nFreeze[g][ZZ])
>    /* Set the mass of completely frozen particles to ALMOST_ZERO iso 0
>     * to avoid div by zero in lincs or shake.
>     * Note that constraints can still move a partially frozen particle.
>     */
>    md->invmass[i]    = ALMOST_ZERO;
>      else
> by
>      if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] &&
> opts->nFreeze[g][ZZ]) {
>    /* Set the mass of completely frozen particles to ALMOST_ZERO iso 0
>     * to avoid div by zero in lincs or shake.
>     * Note that constraints can still move a partially frozen particle.
>     */
>    md->massT[i] = 1/ALMOST_ZERO;
>    md->invmass[i]    = ALMOST_ZERO;
>      } else
> 
> Berk
> 

Minimization with the code replacement produced exactly! the same output.