[gmx-users] mixed solvent energy minimization

Owen, Michael MichaelOwen at creighton.edu
Fri Oct 13 17:47:45 CEST 2006

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)

Do you have any suggestions that can solve this problem?  

Thank you in advance,

Michael Owen

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