[gmx-users] mixed solvent energy minimization

[David van der Spoel]

Owen, Michael wrote:
> Hello Gromacs Users;
> I am trying to equilibrate a box that contains TFE and TIP4P water 
> molecules using the OPLSAA/L force field.
> The system converged several times using the steepest descent method 
> during energy minimizations, but each
> time I attempted a full simulation I received the following error mesage:
> 
> Constraint error in algorithm Shake at step 0
> Long Range LJ corr.: <C6> 2.2606e-04
> Long Range LJ corr.: Epot   -57.2339, Pres:   -325.923, Vir:    57.2339
> 
> I further equilibrated the system using a conjugate gradient, with the 
> parameters described in the input
> pasted below:
> 
> define              =  -DFLEXIBLE
> cpp                 =  /lib/cpp
> constraints         =  none
> constraint_algorithm = Shake
> integrator          =  cg
> unconstrained_start =  no
> nsteps              =  5000
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  0.05
> emstep              =  0.01
> nstcgsteep            =  1000
> nstcomm             =  1
> ns_type             =  grid
> ;deltagrid           =  2
> rlist               = 0.85
> rcoulomb            = 0.85
> rvdw                = 0.85
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> lincs_iter          =  4       
> 
> 
> The grompp program did not recognize "nsctgsteep" so I used the default 
> value (1000) and
> used 5000 steps for the equilibration.  However, the minimization ended 
> in error with the
> following message:
> 
> Back Off! I just backed up traj.trr to ./#traj.trr.1#
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.1
> Source code file: nsgrid.c, line: 226
> 
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
> 
> Variable ci has value -2147483648. It should have been within [ 0 .. 64 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
> -------------------------------------------------------
> 

Try minimizing without constraints first.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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