[gmx-users] equilibration

[Xavier Periole]

> I am trying to equilibrate a membrane-peptide-water-ion system but it
> doesn't work. Gromacs is quite new to me so the questions might be stupid.
> The system should already be quite well equilibrated since it comes from
> dynamics run using amber. The only thing that is done is making a new
> periodic box and adding hydrogens.

1) if your system has been equilibrated in another force field it will need
another
equilibration
2) are you sure it is not taing out hydrogens ?

>
> I have tested to do a steepest descen minimization and the error message
> in the .log file is:
> --------------------------------------------------------------------
> Stepsize too small (6.10352e-07 nm)Converged to machine precision,
> but not to the requested precision (1)
> You might need to increase your constraint accuracy, or turn off
> constraints alltogether (set constraints = none in mdp file)
>
> Steepest Descents did not converge in 15 steps
>   Potential Energy = nan Maximum force:  1.45952e+10
> --------------------------------------------------------------------- I
> have set nsteps = 1000, emtol = 1.0 and emstep = 0.01. I really don't get
> what the "Stepsize too small (6.1035" etc. means? I have also set the
> constraints = none, but nothing changes.
>

There is definitely a problem in your system. The stepsize too small has
been
explained in the list. You'll find it in the archive, see the web site.

>
> When I try to make a dynamics simulation instead the system explodes
> immediately and I get the following error message after 9 steps:
> ----------------------------------------------------------------------
> Fatal error: ci = -2147483648 should be in 0 .. 1880 [FILE nsgrid.c, LINE
> 210]
> ----------------------------------------------------------------------
> When I look at the dynamics trajectory all atoms are out of the box in 2
> steps. Even when I use dt = 0.001.
>

Your system is probably exploding for the same reason the minimization
did not work. Did you minimize in Amber ?

> A question that will be a problem later: I would like to scale the
> temperature of the peptide, the lipids and water+ions separately. How
> should I formulate this in the .mdp file? (How to put water and ions in
> the same group?)
> -------------------
> tcoupl  = Berendsen
> tc_grps = Protein DPPC (SOL Cl)   ?????
> tau_t   =   0.1    0.1   0.1
> ref_t   =    30     30    30
> ----------------------------
>

sounds good.


> The topology file looks like this (Note that in the [molecules] section
> I have commented away the "Protein 1" line. If I keep thath line, grompp
> complains and count the number of atoms in the protein twice!!?? The
> rw-conn.itp file describes the peptide.):
> -------------------------------------------------------------------------
> #include "ffgmx.itp"
> #include "lipid.itp"
> #include "dppc.itp"
> #include "rw-conn.itp"
> #include "ions.itp"
>
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
>
> [ system ]
> ; name
> PMWI (Peptide Membrane Water Ion)
>
> [ molecules ]
> ; name number
> ;Protein 1
> DPPC 64
> SOL 2463
> Cl 3
>

Looks like there is a problem in the definition of your system. In your pdb
or gro file
is the order of appeareance protein, dppc, sol and CL ? That could be a
conflict.


hope it helps
XAvier