[gmx-users] TFE-water minimization

Owen, Michael MichaelOwen at creighton.edu
Wed Dec 6 16:17:43 CET 2006


I have created my own TFE.itp file for a mixed solvent simulation containing TFE and TIP4P water.  To test my TFE file I put one TFE molecule in a box of solvent and and tried to minimize it using the following parameters: 

define		    =  -DPOSRES
cpp                 =  /lib/cpp
;constraints         =  all-bonds
integrator          =  steep
nsteps              =  2000
;	Energy minimizing stuff
emtol               =  0.05
emstep              =  0.01
nstcgsteep            =  1000
nstcomm             =  1
ns_type             =  grid
;deltagrid           =  2
rlist               = 1.4
rcoulomb            = 1.4
rvdw                = 1.4
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no
lincs_iter	    =  4	

Unfortunately my run ends in error with the following message:

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 .. 512 ]
Please report this to the mailing list (gmx-users at gromacs.org)

Can you tell me what I can do to solve this problem?  

Thank youin advance,

Michael Owen
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